Atlus Rep: Also small, but their mascot, Yu from Persona 4 (which is basically their mascot, sorry Jack Frost) is pretty big, and has lots of moveset potential. Additionally, for a series more Nintendo oritented, there is Etrian Odyssey which has tons of moveset potential depending on what class gets in. And maybe finally a black character lol. >_>
Square Enix Rep: Everyone always says Dragon Quest something, but it'd be Cloud Strife more than likely. Its clear Nintendo revelency wouldn't matter for someone that big. SE and Nintendo are on good terms. Etc.
Relevance to Nintendo might still be a factor there; seeing as neither are as universal as Pac-Man or personally connected to Sakurai as Snake/Kojima.
For the former, while an Atlus character appearing as the second Sega rep is possible, I'd still think Jack Frost has more of a chance than Yu. The main Persona games have never been on Nintendo consoles, but Jack Frost appears not only there, but also in the smaller spinoffs and collaborations which have consistently appeared on Nintendo platforms, like Devil Survivor, Strange Journey, SMTIV, #FE and Jack Bros. Along with having a more unique design and greater potential to represent the entire franchise, he's an established character with more history behind him than the protagonist of any one Persona game. Also, P4, huge as it is, will likely be taking a back seat to the spinoffs and sequels of 5 by the time the next Smash Bros. game is in development.
Also, considering how prominent Dragon Quest is in Japan and the strong connection to Nintendo the series has and will continue to have, I wouldn't discount a representative from there so quickly, either. Though ideally a Square-Enix representative would come from the Kingdom Hearts side of things - it's internationally popular, fairly present on Nintendo platforms and has a consistent, iconic lead character; if the rights didn't belong to Disney, it'd more than likely already be there.
In addition, I hope they consider adding third-party assist trophies not from series being actively represented with playable characters to the next game - the likes of Amaterasu, Phoenix Wright, Viewtiful Joe, Neku Sakuraba, Kefka and Frog would have no trouble fitting into Smash, but would never come close to the status required to be considered for a character.