This ... is a wishlist, right? I have given (IMO) good reasons to why gyms should be replaced, whereas the only reason I can see to keep them is simply for tradition.
Also, I don't play side-games. I have played one Mystery Dungeon, it was a nice change of pace, but it was rather forgettable. I'm not going to say that all side-games are bad games (considering I haven't actually played them), it's just that their base concept doesn't appeal to me, which is kinda important in a game.