Hm maybe, Ammy could also run the meter assist too. But I'm picking Ammy because I want to abuse her projectile assist, that thing is gooooodly.
Viper's hyper combos are around average damage. What C.Viper has going for her is great mobility (has an awesome all directional air dash I think) and lots of canceling with her normals, specials and ex moves. She is very combo heavy and they string well into her hyper combos. The only problem is feinting an EX move still takes meter.

I'm actually more curious about the use of a focus attack in MvC3, it prevents her from suffering hit stun at the cost of taking damage, so it's an odd thought.