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• There will be just one site where anyone can ask questions on any topic and anyone can answer any question. But there will be still some universal criteria for closing a question. As someone has said, we don't want another yahoo answers.

• The reputation and other user-specific things will be managed for the whole site.

• Questions will be tagged, just as they are on the present sites. But tagging will have more important roles.

• When a tag will be used in a certain number of questions (say 20k), then some process can be started to define the tag as a "Super tag." It will not be an automatic process. The community will decide whether a tag will become a "Super tag" or not.

• For each "Super tag," there will be a sub-domain of the main site like "dotnet.stackexchange.com" or "webapps.stackexchange.com". Or, "Super tags" could have their own domains. The sub-domain/domain name may or may not be same as the "Super tag" name. There will be specific designs for each "Super tag" as well. In other words, these "Super tags" will become new sites like present different Stack Exchange sites.

• Any user profile/reputation can be queried against a "Super tag" to get a tag-specific profile/reputation. Visitors to "Super tag" subsites will see tag-specific user reputation. For some privileges like chat and retagging the overall reputation will be used while for some other like closing a question will require tag-specific reputation.

• Some special rules can be applied to these "Super tags" if needed.

• Normally a question can be asked under more than one "Super tag"s.

• There may be something like "tag inheritance." There will be a parent tag for each tag. So, [c#] and [vb] will have [DotNet] as their parent. [google] and [yahoo] will belong to [WebApps]; [baking] will belong to [Cooking]. The top level tags will have null. If this cannot be managed, a tag may have more than one parent.

• When a question is tagged with a child tag, it will be considered tagged with all its parent tags in upper levels. So, it will be easier to organize different tags of the same type under one umbrella. And these umbrella parent tags have higher chances to become "Super tags."

• Each user will be able to customize his home page and other pages by subscribing to one or more "Super tags." So he will just see specific types of questions, and the other questions will not bother him, keeping this Stack Overflow ideology in mind: Isn't StackOverflow becoming too generic?

• There will be just one site where anyone can ask questions on any topic and anyone can answer any question. But there will be still some universal criteria for closing a question. As someone has said, we don't want another yahoo answers.

• The reputation and other user-specific things will be managed for the whole site.

• Questions will be tagged, just as they are on the present sites. But tagging will have more important roles.

• When a tag will be used in a certain number of questions (say 20k), then some process can be started to define the tag as a "Super tag." It will not be an automatic process. The community will decide whether a tag will become a "Super tag" or not.

• For each "Super tag," there will be a sub-domain of the main site like "dotnet.stackexchange.com" or "webapps.stackexchange.com". Or, "Super tags" could have their own domains. The sub-domain/domain name may or may not be same as the "Super tag" name. There will be specific designs for each "Super tag" as well. In other words, these "Super tags" will become new sites like present different Stack Exchange sites.

• Any user profile/reputation can be queried against a "Super tag" to get a tag-specific profile/reputation. Visitors to "Super tag" subsites will see tag-specific user reputation. For some privileges like chat and retagging the overall reputation will be used while for some other like closing a question will require tag-specific reputation.

• Some special rules can be applied to these "Super tags" if needed.

• Normally a question can be asked under more than one "Super tag"s.

• There may be something like "tag inheritance." There will be a parent tag for each tag. So, [c#] and [vb] will have [DotNet] as their parent. [google] and [yahoo] will belong to [WebApps]; [baking] will belong to [Cooking]. The top level tags will have null. If this cannot be managed, a tag may have more than one parent.

• When a question is tagged with a child tag, it will be considered tagged with all its parent tags in upper levels. So, it will be easier to organize different tags of the same type under one umbrella. And these umbrella parent tags have higher chances to become "Super tags."

• Each user will be able to customize his home page and other pages by subscribing to one or more "Super tags." So he will just see specific types of questions, and the other questions will not bother him, keeping this Stack Overflow ideology in mind: Isn't StackOverflow becoming too generic?

I have been a member of Stack Overflow for almost a year and a half. Recently I've also registered for SuperUser, Programmers.SE and WebApps.SE. But now I am getting a bit confused maintaining so many different accounts and sites. And more "same-type" sites are coming through the Stack Exchange 2.0 process. All these made me feel like I want to be a member of a more generic site. Just ONE site. Maybe stackexchange.com. So, I have a proposal. You may call it Stack Exchange 3.0. Please go through my full proposal about this new SE 3.0:

• There will be just one site where anyone can ask questions on any topic and anyone can answer any question. But there will be still some universal criteria for closing a question. As someone has said, we don't want another yahoo answers.

• The reputation and other user-specific things will be managed for the whole site.

• Questions will be tagged, just as they are on the present sites. But tagging will have more important roles.

• When a tag will be used in a certain number of questions (say 20k), then some process can be started to define the tag as a "Super tag." It will not be an automatic process. The community will decide whether a tag will become a "Super tag" or not.

• For each "Super tag," there will be a sub-domain of the main site like "dotnet.stackexchange.com" or "webapps.stackexchange.com". Or, "Super tags" could have their own domains. The sub-domain/domain name may or may not be same as the "Super tag" name. There will be specific designs for each "Super tag" as well. In other words, these "Super tags" will become new sites like present different Stack Exchange sites.

• Any user profile/reputation can be queried against a "Super tag" to get a tag-specific profile/reputation. Visitors to "Super tag" subsites will see tag-specific user reputation. For some privileges like chat and retagging the overall reputation will be used while for some other like closing a question will require tag-specific reputation.

• Some special rules can be applied to these "Super tags" if needed.

• Normally a question can be asked under more than one "Super tag"s.

• There may be something like "tag inheritance." There will be a parent tag for each tag. So, [c#] and [vb] will have [DotNet] as their parent. [google] and [yahoo] will belong to [WebApps]; [baking] will belong to [Cooking]. The top level tags will have null. If this cannot be managed, a tag may have more than one parent.

• When a question is tagged with a child tag, it will be considered tagged with all its parent tags in upper levels. So, it will be easier to organize different tags of the same type under one umbrella. And these umbrella parent tags have higher chances to become "Super tags."

• Each user will be able to customize his home page and other pages by subscribing to one or more "Super tags." So he will just see specific types of questions, and the other questions will not bother him, keeping this Stack Overflow ideology in mind: Isn't StackOverflow becoming too generic?

• Users have to keep track of many similar sites. I am now tracking 5 but wishing to register with some other. But it will be tough I think.

• Users get annoyed when questions are closed for being "off-topic". Sometimes even migration to the relevant site is not possible due to the unavailability or immaturity of that sub-site. But in this new system, simply editing tags of a question will suffice. There will be no hassle of migrating questions from one site to another.

• Sometimes people do not know which is the exact place to ask a question. There are many similar types of sites. I have seen same question is asked in different sites and responses are very much different. With an universal community, we may get better answers.

• Choosing new SE sites is relatively difficult. The process is quite lengthy. And after the lengthy process still possibility is there that the new sub-site will not succeed. Then all the questions-answers and other activities are wasted.

Update:
  I think most important flaw raised in the idea is "Ambiguous tag". This happened probably because of my flawed [baking]->[cooking] tag inheritance example. I think it will not be a very problematic issue if users go directly to the sub-domains or "Super-tags". But when someone is asking in the main site, sometimes it IS a problem. Though don't know how much severe. Does anyone has any ideas to solve this? I have already stated mine in the comments.

Update 2:
  I assume people are thinking that this whole idea is a completely different pattern comparing with the present one. So, backward compatibily is almost impossible. But actually backward compatibility is very much possible only with a few tweakings in the tagging. We just have to add some more tags to the questions and that will include them in the relevant "Super tag" or sub-sites because of the tag-inheritance. For example-

I have been a member of Stack Overflow for almost a year and a half. Recently I've also registered for SuperUser, Programmers.SE and WebApps.SE. But now I am getting a bit confused maintaining so many different accounts and sites. And more "same-type" sites are coming through the Stack Exchange 2.0 process. All these made me feel like I want to be a member of a more generic site. Just ONE site. Maybe stackexchange.com. So, I have a proposal. You may call it Stack Exchange 3.0. Please go through my full proposal about this new SE 3.0:

• There will be just one site where anyone can ask questions on any topic and anyone can answer any question. But there will be still some universal criteria for closing a question. As someone has said, we don't want another yahoo answers.

   

• The reputation and other user-specific things will be managed for the whole site.

   

• Questions will be tagged, just as they are on the present sites. But tagging will have more important roles.

   

• When a tag will be used in a certain number of questions (say 20k), then some process can be started to define the tag as a "Super tag." It will not be an automatic process. The community will decide whether a tag will become a "Super tag" or not.

   

• For each "Super tag," there will be a sub-domain of the main site like "dotnet.stackexchange.com" or "webapps.stackexchange.com". Or, "Super tags" could have their own domains. The sub-domain/domain name may or may not be same as the "Super tag" name. There will be specific designs for each "Super tag" as well. In other words, these "Super tags" will become new sites like present different Stack Exchange sites.

   

• Any user profile/reputation can be queried against a "Super tag" to get a tag-specific profile/reputation. Visitors to "Super tag" subsites will see tag-specific user reputation. For some privileges like chat and retagging the overall reputation will be used while for some other like closing a question will require tag-specific reputation.

   

• Some special rules can be applied to these "Super tags" if needed.

   

• Normally a question can be asked under more than one "Super tag"s.

   

• There may be something like "tag inheritance." There will be a parent tag for each tag. So, [c#] and [vb] will have [DotNet] as their parent. [google] and [yahoo] will belong to [WebApps]; [baking] will belong to [Cooking]. The top level tags will have null. If this cannot be managed, a tag may have more than one parent.

   

• When a question is tagged with a child tag, it will be considered tagged with all its parent tags in upper levels. So, it will be easier to organize different tags of the same type under one umbrella. And these umbrella parent tags have higher chances to become "Super tags."

   

• Each user will be able to customize his home page and other pages by subscribing to one or more "Super tags." So he will just see specific types of questions, and the other questions will not bother him, keeping this Stack Overflow ideology in mind: Isn't StackOverflow becoming too generic?

   

• Users have to keep track of many similar sites. I am now tracking 5 but wishing to register with some other. But it will be tough I think.

   

• Users get annoyed when questions are closed for being "off-topic". Sometimes even migration to the relevant site is not possible due to the unavailability or immaturity of that sub-site. But in this new system, simply editing tags of a question will suffice. There will be no hassle of migrating questions from one site to another.

   

• Sometimes people do not know which is the exact place to ask a question. There are many similar types of sites. I have seen same question is asked in different sites and responses are very much different. With an universal community, we may get better answers.

   

• Choosing new SE sites is relatively difficult. The process is quite lengthy. And after the lengthy process still possibility is there that the new sub-site will not succeed. Then all the questions-answers and other activities are wasted.

   

Update: 
I think most important flaw raised in the idea is "Ambiguous tag". This happened probably because of my flawed [baking]->[cooking] tag inheritance example. I think it will not be a very problematic issue if users go directly to the sub-domains or "Super-tags". But when someone is asking in the main site, sometimes it IS a problem. Though don't know how much severe. Does anyone has any ideas to solve this? I have already stated mine in the comments.

Update 2: 
I assume people are thinking that this whole idea is a completely different pattern comparing with the present one. So, backward compatibily is almost impossible. But actually backward compatibility is very much possible only with a few tweakings in the tagging. We just have to add some more tags to the questions and that will include them in the relevant "Super tag" or sub-sites because of the tag-inheritance. For example-