Actually, he and/or the Utroms probably will be in the movie. The ooze that turns them into the TMNT came from the Utroms, the alien race from which Krang originates. Technically, the turtles are somewhat alien in origin, so people don't really have much reason to freak out. I'm sure Bay just didn't really speak knowledgeably about this dynamic of their origin. Liebesman and TMNT co-creator Eastman have cleared the air since and eased tension on the subject.