Yui is a 100% AKB member through and through. Yes, Kyoto and everything, but no - she belongs in AKB.
I disagree that this is a mess. It's something that is overblown due to bias and personal opinions, nothing more. Permanently transfering members across groups and teams would definitely be a mess. But a temporary transfer is like an extended shuffle.
What I meant, Krusha, was that *during the time of the transfer* the girl should just belong to one single team and not two at once. When you have a transfer student somewhere (speaking in "school" terms), certainly this student won't be visiting two schools at once, but just the one he/she has transfered to for the time being. That's how I see it.
Basically like the random transfer stuff we have now two girls just would switch her team memberships for a while. E.g. Ripopo N->A and Yui A->N... once the exchange period is over both girls go back to their original team. Like that.