Boss Battle from Learn With Pokemon: Typing Adventure and Break Point 2 from Mario Tennis 64 are the biggest omissions to me - they'd be perfect for finals at EVO and don't even need a remix
Ai no Uta and Tane no Uta were some of my favourite songs in Brawl, I get why they were cut (copyright/royalties with Strawberry Flower), but it'd be nice to have them back - especially if they had more translated versions.
I'd love a Game Boy Medley to go along with the NES Medley - I'd go with The Prince's Adventure from Frog For Whom The Bell Tolls, Route 1 from Pokemon RBY, Beach from Mole Mania, Muda from Super Mario Land, Final Boss from Wario Land 1, B-Type from Tetris, Overworld from Link's Awakening and Pencilvania from Balloon Kid in any order.
Second the Game and Watch Gallery post, through I'd also want the title theme from the DSi Game and Watch games.
A Drill Dozer medley would be good - I imagine it would mostly focus on Art Museum and Third Gear, but put motifs from other parts of the game in there as well.
Deku Temple from Tingle's Rosy Rupeeland would fit right in with the Swan Lessons and Brewster's Roosts of the game.
Cave from Kuru Kuru Kururin is a very Amiga-esqe track for a 1st party Nintendo game, so it'd stand out quite nicely in Smash. the Touhou-esqe Neo Land track from Kururin Paradise would be good as well.
The PSP version of Galactic Outpost from Pac-Man World Rally is a really good Tommy Tallarico track that's certainly Smash worthy (linked here since it's a hard song to find:
https://www.youtube.com/watch?v=ftahXqDbkCg)
The amount of Sonic music snubs is actually kinda funny - no Ice Cap, no Spring Yard, no Press Garden Act 2, only 1 Sonic R track - but hey, at least we got Seven Rings in Hand!/s
I have no clue why you can't play Lifelight during (non-custom stage) battles.