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A compass to show your orientation, it's annoying to either have to check the map 5 times in a row to confirm you're going the right way or to have to put waypoint markers everywhere you want to go.
A setting that lets you enable or disable the "spotted by wild/alpha Pokemon" music that overrides the overworld music. Of course it should be on by default, but after a while it gets annoying when you just wanna enjoy the background music but something spots you every 5 seconds, plus this wouldn't take away functionality since the eye icon at the top of the screen does the same thing as the context music.
I think Sneasler could have been 100% context-sensitive when the player approaches a steep wall (sorta like how you can't select Basculegion unless you're in water), considering there's no practical reason to ride it otherwise. And for that matter, put the Pokedex as a page inside D-pad up menu, freeing up the D-pad down button so that the other three ride Pokemon can have dedicated buttons. I'm in the postgame and I still take a million button presses to scroll from my current mount to the one I'm looking for because I constantly forget what order they cycle in.
Baby Pokemon are stupidly scarce for what they are, which feels obsolete since the whole idea of them being scarce originally was to encourage breeding for them, which is gone now. Just make every baby as common as Pichu, but have their evolved forms be slightly rarer to compensate.
Why is Cherubi so stupidly rare? I haven't seen a single one yet, and I've been repeatedly going in and out of areas and checking the trees it's able to spawn in. Surely they could've toned down all the Burmy/Wormadam encounters in favor of more Cherubi spawn chances.
Other than these nitpicks (and more general stuff like graphics, which everyone is well aware of), the game is great.