I wouldn't be too surprised if we do have a dozen more megas. They aren't hard to make.
With a few assumptions the process for making megas is probably that the art team comes up with a set of designs with an already made pokemon in mind. Then the team picks the best one and sends it off to be approved and then sent to the guys doing the 3D modeling where they hand it off to someone who then pulls up the mesh for the normal pokemon. Then builds on that mesh and edits parts that change and adds bits that are new. (other than the Mewtwo Y mega which was completely different)
Making a whole new model is a lot of work but building on a previous model can save days of work. Especially with animation and points of movement. (it has been a while since I was in a 3D modeling class, I can't remember the exact name for those)
http://www.youtube.com/watch?v=2WZsZReahfg Mewtwo has got his throne back! BST 780! Take that Arceus!