This whole inFAMOUS vs Prototype debate is quite interesting. 1up have already done three podcasts about it, concluding with inFamous on top. I haven't played Prototype, but I did complete inFamous. However, half way through the 2nd island I just began playing for the sake of completing it and finding out the ending. I didn't enjoy playing the game.
1) The game spans three large cities with many civilians, yet it keeps taking you out of the immersion with the 'level complete' screens.
Plus everything seems very contrived. If you're good, people take photos, if you're bad, people run. Random people run up to you to ask for help. All this sounds good on paper, but in practice it feels like "If X, then do Y" (ie. very simply condition and effect commands)
2) Platforming became a chore due to having to mash X all the time. And it was annoying getting shot from long distances away; the shots would barely damage you but hearing that sound and the screen flashing over and over again is sooo irritating.
3) The world is huge, yet they didn't really do much with it in those three years. Everywhere it's just generic people and cars moving around. I expected a city in chaos (Dark Knight style), but all that happens are either little shootouts between the thugs and the cops, or the thugs and you.
A minor point: My badass character STILL wears that messenger bag?! And that super hero stance throughout the game looked stupid too.