Toughts:
-Geno: I'd like to see him, and I think he is pretty likely.
-Paper Mario: I honestly don't think Paper Mario could fit in, mostly because his franchise has been derailed to the point to lose most connections with the original games. I don't think he would be that unique to play as, mostly because he isn't that different from the actual Mario. I think there are better Mario reps than him: Rosalina, Bowser Jr, Dr. Mario (mostly due to popular belief, and that I main him)
-Skull Kid: I haven't got that far into Majora's Mask, but he's highly requested so maybe.
-Midna: I'd like to see her, but I don't find her pretty likely. (Btw, I think Toon Link could fit well in that list too)
-Zoroark: He/She is pretty popular altough I'd prefer Gardevoir. (Tough, both Zoroark and Garde are pretty unlikely)
-Lip: Same as Midna, I find moveset potential in her, but I find her unlikely.
-Andy: Never played Advance Wars so, no comment.
-Dillon: Same as above.
-Knuckles: I think 2 Sonic reps are enough
-Shadow: Same as above.
-Luffy: 3 Anime Reps are enough.
-Zero: Maybe, but in that case Megaman X should be added (you can easily give him a completely different moveset from Megaman)
-Simon: Simon Belmont? I only played Castlevania 4 so I'm not so sure who he is.
-Chrono: Yes, please. I honestly love Chrono Trigger.
-Rayman: Nah, I never really liked the Rayman series mostly because the franchise's style is pretty inconsistent (that's just my opinion, tough)
-Banjo & Kazooie: I liked the Banjo Kazooie franchise, but I find them unlikely (specially with their Nuts & Bults design)
But what the heck, we can all dream with our fanmade rosters, right?
This is just my opinion, and I'm perfectly sure mine's won't match with everybody else's.