I won't argue Professor Layton, as he's 3rd Party.
As for N, he makes somewhat sense for being a major character in not only B/W, but in B2/W2. However, the fact that his team is never the same (he releases Pokemon) and the fact that the Dragon he gets depends on the version, it may be harder to determine what his team would be if at all.
He could just as easily be a Trainer that actually fights on the battlefield while summoning various Pokemon he has used to assist him, not unlike Yugi in the Jump Stars games.
For Waluigi, he has a bit going for him in that he of all Mario characters (not Bowser Jr., not Toad, not Paper Mario, etc.) was made into an Assist Trophy AS WELL AS as his Dojo update sounding like Sakurai wanted to include him in some way. ("That fact he's an Assist Trophy means he's not a playable character....but Waluigi appears nonetheless!")
Also, Sakurai seems to like Waluigi given that he labels him as a thing going good for Luigi on Luigi's Trophy in Melee ("Things are looking up for the eternal understudy; he's even picked up his own rival in Waluigi.") as well as stating that Waluigi has had many "brilliant game appearances" on Waluigi's Brawl Trophy.
And to be quite frank, Waluigi's chaotic randomness in his abilties would fit the chaotic environment of Smash quite well. If only people would get over the fact that he's another man in overalls, they could see that he isn't like the other three at all...
Takamaru (who this thread is about anyways), I agree, is underappreciated on this poll. I mean, Skakurai has expressed interest in him, and he's been slowly working his way up, with his guest appearance in Samurai Warriors 3, his appearance in Captain Rainbow before that, his game getting a revamp like Kid Icarus got (I mean the updated "3DS Classics" version of the original game, not Uprising) that seems to be planned to be released outside of Japan, and now the references in the upcoming Nintendoland.