how do you transform a mesh over time and and how do you change material over time (gradient transform)
how do you transform a mesh over time
Shapekeys
http://staging.cgcookie.com/blender/cgc-courses/creating-a-werewolf-in-blender/
how do you change material over time (gradient transform)
Depends on your specifics. Couple of options:
Render with two materials and fade from one to another in video editor/compositor
or
Animate the material properties