The devs are not taking requests for new characters, but we can talk about the Clone Engine itself, its limitations, what characters you think will likely be added in future updates, what characters you wish will be but probably never will, and really anything else related to the Engine.
Read about the clone engine here.
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Personally, I think some franchises are over-represented. As much as I would absolutely love to see Skull Kid wearing Majora's Mask as a new character, or a Young Link that puts on the 3 transformation masks, I think we have enough from the Zelda franchise. I think we also have enough from the Pokemon universe (especially considering Mewtwo is almost certainly going to be added). Basically I want new franchises.
So I've got 3 characters I would really love to see be added to Project M:
Megaman
He's already gonna be in Smash 4, he's super hype, and he's awesome. The moveset possibilities are great; taking powers from all the games he's been in and stealing moves from Smash 4.
Isaac (from Golden Sun)
I love Golden Sun. Isaac has a sword and has Psynergy. Awesome. Lot's of material to draw from to create a moveset, just like Megaman. People have been hoping for this one for years. We also have the Assist Trophy available for the model and some animations, if that's a thing that's possible to take from.
Someone from Castlevania
I don't really care which character. Peronally I really like Soma Cruz from Aria of Sorrow or Alucard from Symphony of the Night. Whip weapon is currently under-represented in Smash. Lot's of powers to choose from for a moveset (are we seeing a pattern here?). Caslevania is very popular. We already have a stage!