The 2K/Rockstar thing is largely down to the Housers, I think. Those are two guys who value independence above all else. While 2K could wrestle control from them, they've made the very wise decision to give them as much as they want and keep them sweet because if they leave Rockstar would probably collapse. Rockstar run their own PR departments and everything. It's also working - their ad campaigns and such are hugely successful. It's working, so why fuck with it, right? They also want to avoid being in the kind of situation Acti/IW was in, I'm sure, and who can blame them?
Square Enix could've taken this approach but it's expensive - and it probably is wiser to be thrifty right now. More than that, though, it gives the image of a company segregated. The quality of a Rockstar game doesn't influence my decision to buy a 2K game because I know they operate as very separate entities. The whole point of fully assimilating the Eidos brand into SE and turning Eidos into a label is to project an image of a truly international company.
We don't really have a properly international dev - EA partners with Japanese devs but has failed to have success with it. Konami, Capcom and Nintendo have all had limited amounts of success with direct work with Western studios like Blue Castle, Rare, Retro and Mercury but aren't pushing forwards on expanding that strategy as fast as they perhaps should. Sony are the exception with a strong international development culture, but even with them there appears to be this great big rift between SCEJ and SCEA/SCEE. Worse, SCEJ appear to have like SEJ lost the ability to actually finish a HD game without compromising it in some way.
I think Wada's vision is to be the first truly international game developer and that could be massive for them. It's a good move. Everything points to it, from the hardcore focus on Eidos this year and last year at E3 and other Western shows to the fact that the development studio for their next-generation tools that'll power the next FF/KH/DQ is made up of 50% Western people drafted from Eidos, IO and other places and also in places based off tech pilfered from IO's new Glacier Engine - they want to standardize the business. Good luck to them; I'd rather SE survives and has other ways of making money, because if they do the future and safety of FF, KH and such is more assured, and it allows them to take chances with development on more niche projects.
This is a more personal opinion thing thing now, I suppose, and not everyone will agree, but I'd rather SE made lots of money out of Hitman/TR/Deus/Thief/Just Cause/Kane & Lynch/Kain (see what a fucking strong list that is?) and be confident enough to make more niche FFs than keep chasing the train of trying to streamlining in search of wider success which I think has overall been detrimental.