The core difference in one sentence
Viggle is built around characters doing motion: you bring a character, and movement comes from templates, prompts or supplied motion sources. Genjutsu is built around footage being rebuilt: you bring a clip you already shot, and the motion, camera and timing of that clip are the anchor while references replace who and what appears.
That one difference decides most comparisons, because it changes which projects each tool is right for - and it is why the honest answer to "which is better" is "for what".
