I'm not sure if this poses that much of a problem. We have "canon" designs for the Pokémon trainers, as can be seen on the scans of corocoro. I'm assuming they'll be using those in the next installment. Pokémon is one of the biggest franchises of Nintendo. It'd be a shame to leave them out of the next SSB.
The Avatar doesn't even have an official artwork (except with the hood on), that's why I think the designs for the trainers are more "canon" than the costumisations of your unit in FE.
And although I'm only half-way through FE:A, I don't see why Chrom isn't a main character. Maybe not the main character, but definitally a main character. He, or Lucina, might just as well be there to fight alongside his ancestor.