There are some serious issues with the PC port of Prototype 2, from what I can gather.
Most people who have complained about the game's performance have been running on ATI graphics - I'm not sure that 100% of the people having issues are ATI'ers, but from my sample size of probably 20-30 people, I've found most nVidia graphics users to say "it runs great!" and most ATI graphics users to say "Wow, this stinks!"
I went through and collected and collated all the suggested solutions to the problem over here, on my blog but the #1 thing that actually helped me was setting the processor affinity.
If I use Task Manager to force the processor affinity of prototype2.exe to only core 0, the game runs smoothly without issues. If I don't, then I get all sorts of performance issues - sometimes the input lags, often times the frame rate drops like a rock, etc.
If that doesn't work, you can try some of the things that others suggested and had good luck with, but that's where I'd start.