-A remix or something of Super Mario 3D World's World Bowser/World 8 would've been nice. It's my favorite track from that game <3333
-Dialga's Fight to the Finish! from Pokemon Mystery Dungeon: Explorers of Sky/Time/Darkness would have been perfect on the Kalos Elite 4 stage
-I would take Pokemon Black and White's Trainer Battle music over X and Y's any day of the week, any week of the month, etc. etc.
-Pokemon HeartGold/SoulSilver's Red/Lance battle should've been on Pokemon Stadium; it's just too good to leave out. ...They left it out anyways.
-Adventure's End from Mario and Luigi: Dream Team would've been soooooooooo much better than that horrendous remix of Try, Try Again.
Those are really it. I'm perfectly fine with the soundtrack as of now (other than the previously mentioned Try, Try Again remix ((seriously, why'd they make such a good battle theme so bad???))). These are just a few that are my personal favorites and it would've been super awesome if they had added them.