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.
I loathe calling this a situation where the sister-groups got screwed over. Why? How? Because you think Miorin and Minarun are shit members? In this case, due to the two of them obviously not being top level front girls, what about AKB getting Ripopo and Annya? Those definitely aren't top level front girls. Yes, AKB got Milky and Jurina too, but in Jurina's case, she's been in senbatsu since Oogoe Diamond. And it's to be expected considering Akimoto's vision, that sister group members finds their way into senbatsu.
This time around AKB got Fuuchan, Haruppi and Nao, three very popular girls, yet they lack that super-exposure that makes them well known to 'everybody'. Going to AKB can help that. It certainly won't work against them. And as such this both benefits AKB in getting new girls from sister groups, it benefits the girls being transferred as they get valuable experience, but it also benefits their original groups who now have even stronger members in their groups.
Unless we're talking borderline irrational otaku-hate, i.e., anti-behaviour, this can work out splendidly just as any other imaginable mix-up by transfer of whichever girl to whichever team. The reason is they are all Japanese girls in a specific age range, managed by the same company and set of producers following a very specific work philosophy applied to these groups, i.e., the 48 family.
That's why when considering that the girls will most likely try to do their best, as will the teams, and the producers, we will most likely get good results as well.
The first mix wasn't a failure, save for Kitarie's bumpy road in SKE - but recently she was warming up quite well in SKE, with the girls considering her just as much a full-fledged SKE member as themselves (just watch Budokan concert for reactions from them and her).
The permanent transfers of Sasshii and Rabutan are different. Different due to circumstances, both over a longer period of time, and sudden unexpected circumstances.
Rabutan was arguably stagnating quite a lot in AKB, with nothing to offer and nowhere to go. By sending her permanently to HKT, she goes from being the growing up loli, to the most senior member in the group - a veritable granny, hilariously enough. Thus she takes on the role that Nacchan, Shihonabe, and in particular CinDy had - when going from Team A - to Team B. And this gives her ample opportunity to grow quite a lot. We know very well how important CinDy for instance, was to Team B.
As for Sasshii, whatever was the original reasoning for her transfer to HKT is hard to know now but (though we can easily speculate of course), her development from a rather unknown undergirl that mostly hardcore fans followed, to becoming hetare queen, and from there on out becoming super-skilled as a host, MC, variety talent, and more has been spectacular. Her team spirit and team dynamics understanding is really something else, and we can see this easily in HKT. That she became co-theater manager was a hilarious shock, but it's actually understandable.
So, while these temporary transfers aren't as "drastic" as the two HKT transfers, they still serve a purpose. And it's both on an individual level (the members themselves), and on a team/group level. Call it cross-pollination if you're botanically inclined.
In the end I think they can shuffle with any one member from any one team to any group they see fit, and it can still be good, depending on how they execute it.