A villa would be awesome, though I would be surprised to see it. It would be neat if we could alter the architecture of the villa, or at least the paint color, alter the plants (not just berries, but other trees and such), put up furniture, etc. That seems more like something to expect from Animal Crossing than from Pokemon, though, and I suspect we've come a long way just to get customization back. But even larger secret bases with more space for decorations would be nice. I was disappointed that I couldn't coat all of my secret base floor space with decorations in AS.
Re: having things all "come together," that could suggest a return to secret bases and such, or a slight upgrade from that, though I still wonder if villas would be going a bit too far. But I won't rule out the possibility until we've gotten more info about the games. My sense, though, was that by bringing everything together, it was more of a reference to the series coming full circle. Now gen I can connect with gen VII, and old fans and new fans can enjoy the oldest and most recent entries together on the same system. I do think there will be a return of some popular old features, but I wonder if some of the coming together element is just a marketing ploy. Still, I'm excited for the games, and eager for more information at this point.