There are too many (similar) stackexchange sites! Reasons why this is bad:
- Waste of resources (it would be easier to manage and maintain to have fewer)
- Difficult to choose which one question is best suited for (example1, example2). For a non-tech example, is Why is bench pressing your bodyweight harder than doing a pushup? really a physics question or more about Physical Fitness? There is a lot of overlap, for example there is computerscience, theoretical computer science, and computational science. Furthermore stackoverflow has tags that would make many of the questions on this site be suitable for it.
- Question may get migrated to a site you don't have an account for (example) and may accumulate down and close votes.
- Smaller community base means fewer people are reading the questions and as such the chance of quality answers goes down
- Diffusion of responsibility (example)
- Sometime questions may be asked with the hope of getting different perspectives and since posting the same question to multiple stackexchange sites is not allowed, this could be a problem. Say for example you want to design something that is user friendly and secure. Different answers we be given on http://security.stackexchange.com vs http://ux.stackexchange.com
- problems with migration, such as rejected migrations.
- more difficult to search for questions/answers. Now each possible site must be checked to see if the question was asked. (for example you wouldn't normally think to check both health.se and skeptics.se for the same question)
I'm not saying there should only be one site, I am saying there should be fewer and beta sites shouldn't be created so liberally and that the boundaries between sites should be more clearly defined. I've heard a counter argument to this is that subsites were created as a response to new rules being made giving a smaller scope to Stack Overflow. This is not properly addressing the issues, those rules should be changed.
Another example is, if someone is trying to setup and IDE on a Mac, should it go on super user, apple exchange, stackoverflow or programmers? It may not be known to the individual if the problem is specific to Mac or the IDE in general. Furthermore, we're now starting to split sites into various languages.