Okay, got some more ones (and putting in the two I had before)
Airship (Super Mario Bros 3): This would be kinda low prioty, given we technically have both the main remix and the bit in the paper Mario Medley, but I feell like Brawl's is to metal-y. I would prefer more orchestral "bringer of war" quality a la galaxy, but at that point maybe it would be too close and just be redundant. Plus, two (unless they're one medley) SMB3 tracks are already confirmed.
Egg Planet (Super Mario Galaxy): While I do like the starman and underground bits in the wii U remix, the song really should get to stand on its own seperate from SMB1)
Obstacle Course: (Yoshi's Island): The same sort of reasons as Pixel gave.
Yoshi's Story Level 1: Reasons given from Before.
Ashley's Song: (WarioWare Twisted): Sort of a weird example of a request, but I almost hope that ver. 2 gets an English ver. solely because that would mean we get the song. Even if we just got the Japanese one only I really wouldn't care; It's more just a matter that I don't like how there's a region exclsuive song.
Norfair: (Metroid): I would perhaps like something closer to Zero Mission's more grand version. While I like the techno approach of brawl, I'm not sure it's really what fits Norfair as an area.
Smashing Song of Praise (mother 3): Well, not really the song itself exactly (notice how unfounded revenge is gone): I Actually want wasteful anthem more; while "Smashing Song" has "more" to it, I feel like wasteful anthem's lack of distracting side sounds is just generally better. That said, I feel like, if somehow there was a magic limit, I would not want a pick "wasted" on this instead of an actually new song.
Onett Theme: (Earthbound): Kinda similar to above song. I would love this dsconnected from Winters. Though, I guess the onett bit itself is good, so I'm not sure if I should pick it.
Big Blue (F-Zero): Reasons from before.
Meeting Theme: (Geneology/Tharcia 776, and Sacred Stones versions): There is the meeting theme medley, but personally, I almost wish the version from geneology got in (mor specifically because I like the version in Tharcia 776). Sacred stones' vesion is pretty sick too. That said, the meeting themes are pretty short so they probably can't get in as their own, and I do think their remixes in the medley are good.
Tetris Type A: Kinda obvious source. Something about the instrumentation of this song and how it seems to built slightly "spooky" for luigi's mansion always felt kind of odd. I guess I picture a more upbeat remix perhaps?
Battle Scene/Final Boss (Golden Sun the lost age): I admit I haven't played the original at all and I've listened to the source very little, so for all I know the remix is accurate, but I just never liked the style of this song.
Minor Circuit: (Punch Out): The wii U remix just uses a bit too much "electric" to me, something about it just doesn't quite feel okay to me i guess
Lastly, for Smash original songs,
Metal Battle 64: Cause seriously, this one is amazing
Fighting Polygon Team: Same as above
Master Core: For some reason, I would like to see what this song would be like if it was turned into a standard battle theme
(Also, if songs only with a direct port count, I would like SMB2 USA, Ricco harbor, battle for storm hill, Ruins from Wario Land: shake it, twilight princess hyrule field, hidden village, Dragon roost village, molgera battle, village of the blue maiden/kakariko village, checker knights, Frozen Hillside, Planet popstar 64, Metroid Prime 2 multiplayer/Green brinstar from super metroid, Champion Diantha, Space battleground, Dream Chaser, climb up and get the last chance, Shotgun Kiss, Conquest (ablaze), rockin' K.K., K.K. Condor, The actual version of Skyworld from kid Icarus (technically in the 8-bit medley), Kid Icarus Boss Fighy 1, some of the famicom medley songs in brawl that haven't had their games touched yet, golden forest 1080 snowboarding, mischeivous mole way, theme of solid snake, some of the stuff in the namco medlies to receive actual remixes, let the battles begin, RIders of Light, After Burner Climax Mix)