Legit Threats
Ra Al Ghul
Clayface
Prometheus (Not really a core villian however)
Solomon Grundy
Poision Ivy (If she gets the jump on Stark)
Deathstroke
Otherwise You would have to give extremely one sided prep to the majority of Batman villains in order to outsmart Stark. The guy is one the smartest people in the Marvel U. who has prep for fights against the likes of Thor, Hulk, Rulk, Magneto, and The Phoenix Force.