i know some are molded so that they don't fit in other powermasters, but is there any standard size to most of them? like, are they any that would fit with powermaster prime?
They are standard size except for Doubledealer's since his are molded to unlock either his Autobot mode or his Decepticon mode.
So they were mix and match basically. The idea was kinda revisited with the minicons in Armada. Use the smaller robot to unlock features of the bigger robot. Seems like they thought it would be better to have them turn into vehicles/animals than just engines and also to have them unlock special features instead of the transformation itself. That way you could still play with the figure if you lost them or they could have play value by themselves.