While I definitely wouldn't argue that Square or Nintendo give two shits about Geno, I don't think this is the best example--Square wasn't involved in any way shape or form in Brawl, so no original character from that game could appear in any sort of form even if they wanted to.
A better example would be Fortune Street, which was made by Square and actually has a music track from Super Mario RPG in it but it contains absolutely no references to it beyond that (opting instead for "filler" characters like Daisy, Birdo, and Waluigi).
EDIT: The Basketball and Sports Mix titles as well, which are rife with Final Fantasy references but absolutely no SMRPG references.