Holy carp, I love how much thought you put into this.
I particularly like Animation and Energy constructs. Though the former should be fleshed out a bit more. For example I animate a nearby chair (Or hose, or Telephone Pole, and have it attack someone.)
Do I use my stones to make it attack, does it get to use the stones I am giving it, do I have to use an action to make it attack or does it have it's own action? Do you use the area of effect chart for large objects, would that require extra stones or just be up to the AN? (I am already imagining an enemy animating a building or a bus) One fun option at a + to cost would be to change the object's shape while it is under your control, ex the car you control turns into a robot . . . fun for nanotech powered characters.
Some of these could be used, some of them is already in MURPG 2.0 and others would proberbly not fit, because they are to unbalanced or not explained to well. Like Death Touch which only costs +3 and allows me to kill someone with a simple touch (or thats how I read it since it doesn't say how the power works).
But Animation and Body Part Substitution doesn't sound bad at all, however, Body Part Substitution sounds rather expensive for a flavor modifier.