Question: Does anyone know why Gambit was featured less and less in episodes as the show went on? He was one of the most popular characters in not just X-Men, but all of Marvel Comics around the time this series first aired, so unless it had something to do with his voice actor's contract, it seems odd they wouldn't have utilized him more.
Answer: Chris Potter, the original Gambit voice actor, did indeed quit the role in the 4th season. His last episode was The Phalanx Covenant Part 1 so it seems reasonable that Fox would limit the use of the character even though it was recast. It doesn't appear that Potter left the role due to animosity, he stated in an interview that he wished to play Gambit in the first live action X-Men film.
Answer: Because he stole a chemical from his lab.
But Batman knew that with it, Clayface could permanently retain his shape and Clayface desperately wanted to be Matt Hagen again. In a sense, Batman stopped Clayface from becoming human.