So, moving away from the huge Nintendo all-star Snake (seriously, he's so close to Nintendo, Konami should give the series to them) and the guy who doesn't have any importance to Nintendo whatsoever (Simon Belmont), Square-enix was brought up in the SmashGAF IRC, and with the introduction of the customizable movesets of the Mii Fighter and Palutena, I've had an idea.
The only 2 series from Square-enix that are truly popular are Dragon Quest and of course Final Fantasy - the latter more so globally, while DQ is significantly bigger in Japan than the rest of the world.
Final Fantasy is a series in which every game is its own contained story and world. So, I believe that picking a single characters from one of those games would not do the franchise any justice. There are a lot of elements that tie them together aside from the name, such as several mechanics, species (Chocobos, Moogles, etc.) and of course the class archetypes.
My suggestion was to make a character loosely based on Final Fantasy 1. It could either be a human (you could name it the Warrior of Light, based on the Dissidia Final Fantasy incarnation of the FF1 characters), or a Moogle/Chocobo. Then add to it the most iconic jobs of the franchise, and based on which job you give your WoL/Moogle/Chocobo, we would have a different moveset. It could be involving Fighter/Knight, Black Mage, White Mage and Ninja (cause I feel it would offer more variety than Thief), perhaps even Black Belt/Monk or some of the other less known classes (tho I feel like the Red Mage wouldn't offer enough deviation from the other 2 mages), and you'd be good to go.
Final Smash could be summoning Shiva, Ifrit or Bahamut or something, idk.
In any case, I feel like that would probably the best solution to represent Final Fantasy, if it ever were to happen. I always felt that picking a single character from a specific game or a single class (since Black Mage was often suggested) goes against the whole variety aspect of the franchise, especially those games that allow you customizing your characters, which is a mechanic that spans across most of the series.
I haven't played enough Dragon Quest games to give any insight in that, though.