I very much liked this game! It was great for a sandbox, and the powers were so much fun to mess around with... and the art in the cut-scenes was so.. OMGAH *drool* So gorgeous, and graphic-novel ish. I finished the game a while ago following the "Good Reputation", still have yet to finish it following the "Bad Reputation".. and then, on to Infamous 2!
I have problems with doing bad things in video games too (wheter they are labeled as 'evil'/bad or not in the game, if something in the game goes against my morals it's so hard for me to do it, even if it's "just a game"...), so I know how it must have been for you playing inFAMOUS At least the karma stuff in inFAMOUS gave more sense than the karma in Fallout...
ASDF. dying from the beauty. Infamous was better in my opinion. Alex was overpowered. Way too overpowered. And it got boring so fast - Basically the same thing over and over again. Cole was more interesting. He was reasonably powered and the environment was balanced with his powers rather than him exploding everything just on impact. The game is more challenging.
BUT JUST MY OPINION (and a very late one at that). I played both, but Prototype basically got so bland I nearly cried my eyes out. OTL