Since he has no supporters and because he didn't originate from a video game he would have zero chances for Ultimate, which is unfortunate considering how his teammates from the cartoon and comics are already here in Smash
. Duck Hunt has someone acting as the player using the Zapper Gun, so if you substitute Captain N's dog Duke for Duck Hunt then the person using the gun could just be Captain N playing Smash this whole time with his own Zapper. As for Palutena, apparently Lana's design took some minor inspiration from Palutena's classic appearance. Maybe it's because the show didn't have the royal damsel / love interest character and they couldn't use Peach and Zelda?
Captain N would be perfect for a Subspace mode because you could just have him being warped into the game and work with videogame heroes and icons against the antagonists, similar to the source material.
I doubt Nintendo would ever do anything with Captain N ever again but if he were to get the Pit treatment and get an updated design and a game then there's a lot of crossover potential that Nintendo could do with him. Captain N pretty much could be Nintendo's Kingdom Hearts but you'll travel to videogame worlds (primarily Nintendo owned IPs).