I got both games and I feel that infamous has some technical polish that prototype doesn't have. However prototype has more polish on its story with rendered cutscenes (although I really liked the infamous way of cutscenes) as well as the interesting memory cutscenes that use live action instead of ingame or rendered cutscenes. I also feel that the writing in prototype is better.
If I could only afford one, I would have gone with infamous. That could be my sony fanboy in me but I got really hyped for it (and prototype) before its release.