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Have NPC's react differently and say new things to you while the game progresses. Have them acknowledge your achievements, or shit on you for doing something they feel was wrong. Make something happen on major holidays, like make some cities Christmas themed around that time of year or something. Make the customization more robust by letting us choose between some different heights, builds and ages. How about re-introducing seals but making them more noticeable and easier to get?
Maybe have spotpass secret bases/houses where you can invite people on your friends list and them and all the pokemon your in your parties can just chill in a chatroom sort of thing with minigames.
I dunno, I just want more side content to make things more enjoyable and more oline features that aren't just competitive battling or trading related.