Stack Exchange has grown to consist of over 130 sites, that discuss a variety of subjects. We still call ourselves a single network. Apart from the fact that the basic functioning is the same, there isn't much 'association' between the sites (that I know of, except for Association Bonus of 100).
There are a lot of links between the subjects discussed on the various sites.
For example, there are various physics questions that require a higher level of mathematical understanding. Yes, these questions may be off-topic on the maths site, but a person answering it on the physics site should receive some rep on his math account also. Someone answering a question tagged 'physics' on the maths could receive reputation on his physics account also.
Similarly, someone answering questions on the web applications site could also receive reputation on his main SE account. This will help since there are many computer-related sites (main, programmers, stackoverflow, code golf, etc.), with only slight differences in accepted questions. There should be an option of posting a question on 2 or even 3 sites, if it fits the criteria for all of them.
I currently know that only that only the association bonus links the sites, and reputation, badges, moderation, etc. are all kept separate. Please correct me if I am wrong.
Will this lead to over-complication, or is it a good idea? It is only an 'idea' that I got, how it could be implemented is completely upto the community.