You said morph materials... in ProAnimator, the word materials means the surface attributes including color, texture, transparency, etc. If that's what you mean, you can accomplish the effect in a couple of ways. 1) by creating a movie that transitions between two still images and applying that movie to the surface of the objects. Or 2) You could accomplish the same effect by rendering your animation twice... once with each material you want, and doing a dissolve between them where you want the change. It's totally controllable and becauuse the animations match exactly, the only transition you see is in the surface attributes. This second way is probably easier and more flexible.
If you meant you want to morph the actual objects, that answer is also yes. You can morph objects overtime by using a technique called layer cycling. It works by creating a multi-layered Adobe Illustrator document with each layer representing a frame in the animation. You can use the blend tool to create smooth transformations, then break the blend apart and assign each version to a different layer in Illustrator. You could also do this work by hand if you need to. ProAnimator (or Invigorator Pro) can both use layer cycling to create a series of 3d objects based on the Illustrator art. You cannot use this technique with imported 3d objects.
As for mapping movies to objects, it's pretty simple. On native ProAnimator objects you can also determine which faces of the objects get the movie applied and which don't.
Please feel free to download a demo of ProAnimator and give it a try. If you get stuck, post a question and we'll try to help.
ProAnimator will let you use video for any of the texture maps. Color, bump, transparency, etc.
It even has controls to set the start time for the video to play back. This enables you to put video onto an object's face and have it hold the first frame for, say, 2.5 seconds until that object is visible onscreen.
Morphing (blending) from one material to another can be done with creative use of texture maps. For instance changing an object from red to blue would have to be done with a movie of red turning to blue, used as a color map. Another way that would work would be to duplicate an object once it was animated so you had two identical objects moving identically. Then you'd make one object red and the other object blue and use a Visibility Action to fade between the two.
It's funny when this happens... two people writing answers at the same time.
Using a visibility action is a great idea, Zax. I hadn't thought of that one. You could make it even more cool using the cascading visibility slider to cause the morph betwen materials to progress from one object to the next one during a pose. I wouldn't want to try that any other way!
You can accomplish changing the scale and position of a movie by using the ProAnimator plug-in inside of After Effects. You would use a precomp to scale the movie and can adjust the x and y offset from there.