There should be characters from franchises that Capcom never own, but licensed to make games (Yo!Noid, Cadillacs & Dinossaurs, Disney, D&D, JoJo's Bizarre Adventure).
As for others, let me see:
* The Grandmaster (Strider);
* Ton Ton (Son Son);
* Arma (Demon's Crest);
* Bilstein (Star Gladiator);
* Any character from Giga Wing;
* Santana Lawrence and Mary Miyabe (Cyberbots);
* Any character from Armored Warriors;