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ultra necrozma is in battle only meaning no petting and feedling and no way to permanently heal necrozma. my biggest disappointment, fuck gamefreak for not letting me give the crouching prism hidden dragon a tummy rub.
ultra megalopolis is just a hallway and has no revisit value. kind of expected this but i'm still disappointed
blacephalon and stakataka are postgame only. the quest is nice but short and inconsequential really.
alola being shrouded in darkness and necrozma capturing solgaleo and lunala is only about 5% of the game. would've been cool to be forced to continue the campaign while the light was stolen for a little while and see the alolan people's reactions
more with the urs, especially in terms of improving their battling skills as the story goes on. maybe in postgame we help them evolve poipole, or they capture more ultra beasts because they were studying your battling skills and thought "hey, that 6-man team thing seems to work pretty well right?"
those are the biggest disappointments i can think of but i think all those have been discussed to death.