Geno. I could actually see him being an assist trophy though, as sad as it would be. I'd legitimately pour one out for the Geno fans if that happened.
I could see easily Shantae getting the assist trophy treatment. Similarly, Klonoa or Agumon are both important characters, but lack wide relevancy or popularity. Phoenix Wright and Professor Layton could both be reduced down to Assist Trophies similar to Dr. Kawashima. Jack Frost could make for a good assist trophy representing Atlus. Slime or Chocobo/Moogle could represent Square Enix in a similar way, though Sephiroth casting Meteor and doing stupidly OP **** is the dream. If not playable, Steve could be an assist trophy, though I feel like the Creeper is more likely. Series assist trophies I could see happening would be Riku or Xigbar (KH), Yosuke, Futaba, or Rise (Persona), Collete (Tales of Symphonia), Edgeworth (Phoenix Wright), Vergil or Trish (DMC), Gruntilda (Banjo & Kazooie), and the list goes on.