Bomberman: He's been appearing mostly on Nintendo consoles ever since the NES days. Konami owns him now, and I think he would fit much better than Snake.
Bombeman wouldn't be a bad fit but Konami probably wouldn't go for it. Goemon might be a better choice for a secondary Konami guy though.
Simon Belmont: Castlevania started on the NES and while the franchise shifted towards Playstation for a while, the series has thrived on Nintendo's handhelds. The series has a lot of protagonists, but Belmont was the main character in the first two games and in Super Castlevania IV (which was actually a remake of the first game). But do you go with Barbarian Simon, ginger Simon, or Prince Valiant Simon?
Simon is easily the important 3rd party rep that's missing. I would imagine he would look similar to his SCIV incarnation since that it would fit in pretty well with Link and the FE characters. Any look is fine aside from the later ones really(kojima, LoS, Judgment)
Pete/Jack: Who? The kid from Harvest Moon! I thought his name was Jack, but some people say that his official name is Pete. WHATEVER. Anyways he appeared in the original game, the 64 version, all the GBC games, and the GBA game. Harvest Moon has mostly been a Nintendo only franchise and the series is still kicking today.
I don't think Harvest Moon reps are really iconic enough to make an appearance in a dream match like this.
Professor Layton: If they want to pick a more recent character, Layton could work. Level 5 develops a lot of games for Nintendo platforms (thanks for DQIX by the way) and he would be a great DS representative. I always like the inclusion of non-combatant characters in the series.
Phoenix Wright: In the same vein as Layton, he is a non-combatant that has shown up mostly of Nintendo handhelds. He did appear in MvC3 though.
I guess I can see them as being important as far representing DS goes but I just don't think they're important enough to waste guest spots on.
Chocobo: I was trying to think of a good FF representative, but none of the leads really stuck out. Why pick Terra over Cecil for instance? But then I realized Chocobos are in nearly every FF Nintendo game, and some games of the Chocobo series even appeared on the DS/Wii. It would be a good cutesy character, maybe a rival of Yoshi.
Slime: Similar to Chocobo, slimes are an iconic part of Dragon Quest which got its start on Nintendo platforms (and then came crawling back). There are so many different types of slimes, so I think you could have a lot of diversity with its moveset even though the character's appearance is as simple as can be.
FF and DQ reps would fit in but picking a rep seems like a hassle. Slime and Chocobo are pretty mascot-y but I'm sure how much people would to play them.
Ryu Hayabusa: Kind of a stretch. I mean Ninja Gaiden did start on the NES, but the franchise hit the big time with the Xbox reboot. Ryu has appeared in Ninja Gaiden DS and NG3 was on the Wii U though, and Tecmo is very close with Nintendo. I want to see him fight Greninja.
Greninja has pretty much squashed any hopes I had of Takamaru getting in and Ryu is even likely. We are just far too removed from his NES incarnation these days.
Contra dudes: I have no idea what their names are... the dudes! The dudes from Contra! I think they could be similar to Snake, but with crazier weapons. Contra has mostly been on Nintendo platforms throughout its history, even showing up on the Wii and DS.
Simon and Goemon are much better reps as far Konami goes.