I think Simon Belmont makes the most sense if one needs to be 3rd party. We already have Dracula's Castle, and Castlevania used to be a big thing for nintendo. I know very little about Castlevania, but odds are there's something that could be made out of it.
Other good choices in my opinion... Harvest Moon is unlikely to be in SSB4 but is fairly popular on nintendo consoles, Jack maybe? Battle Network was almost exclusively Nintendo based, but Capcom could be a risky call
If we're going specfically to use characters from third parties already in brawl (read, Sonic or MGS), I'd suggest Chaos, Dr Robotnik or Emerl for Sonic's choices. Emerl is the least important of the three, but could provide some interesting gimmicks with it's own version of an ability absorption like Kirby's hats.
MGS... Big Boss or Revolver Ocelot could serve as interesting choices, I'd love to see a Metal Gear Rex in as a PC at Giga Bowser's scale, but that seems... unlikely.
(on an unrelated note, I found an old moveset (from A attacks to taunts and victory poses) of Meowth, as well as a few others, should I post them?)
Edit: (Ok, the Movesets I have are
Meowth
Snagem Trainer Wes (simplified to Espeon and Umbreon for a theoretical Project M)
Spike (Ape Escape, PS1 game, long story)
Piposaru ("")
Master Chief (More of a joke than anything real, constrains to brawl's "NO real guns" rules)