This was an odd choice... Fallout 3 would be what i would choose, it has longevity, great depth and atmosphere but is also fun, you have to keep your eyes open as you WILL miss things if you run through it without exploring. Never played prototype but never will either, it's one of those shallow action games that appeal for a short time before you trade in again.
Curious, if your stuck for choice why not get both, Fallout 3 + expansions shouldn't cost too much and i'm sure prototype is on the cheap now.