They're two very different games, inFamous is more of a sandbox game, whereas Prototype is more arcade-beatemup style (though it has sandbox elements as well). inFamous powers are all mostly electric, whereas Prototype has mostly biological powers. inFamous has a few distinct abilities (that all feel very satisfying), Prototype has a very large selection of upgrades (the first mission unlocks at least 20).
That said, they have their ups and downs.
inFamous:
The Good: The city really makes you feel like you're in a city where something's bad happened. It's smooth, it looks dirty and well, like a city. The people will interact with you body on your reputation (huddling to take pictures of Good Cole or throw stuff at Bad Cole). The powers feel VERY satisfying. Lightning Storm really feels like a destructive force being unleashed, you really get a feel of speed when Induction Grinding, explosions very real and interact with your sound and vibration VERY effectively.
The Bad: The game is glitchy at times. Graphical issues, sometimes Cole fumbles around when you are trying to heal/drain a person on the ground. It occasionally gets repetitive, but the sheer variety of the side missions makes this much more minor than in a game like Assassin's Creed. Morality is pretty cut and dry, and with the exception of one mission I always knew which choice to make for the 'good' path. You basically just decide from the beginning of the game and stick with it. Evil is more fun.
The Ugly: Not much, it's a very pretty game, and is about the caliber I expect from most next-gen games. Not Uncharted quality, but not ugly either.
Prototype
The Good: If you are into action, Prototype has action on massive scales. It regularly reaches a level of chaos that inFamous only hits in a select few missions. There's some fun powers that work more on form shifts and melee combat than infamous. If you like more melee combat and feeling like a god, than Prototype may be better for you. inFamous you feel powerful, but not really omnipotent (rockets still nearly instant-kill you through a large part of the game) and you can be hurt. Prototype, it takes tanks and helicopters to bring you solidly down. There's so many upgrades, you can spend a lot of time working on getting them, some feel very satisfying.
The Bad: It gets more repetitive than inFamous. Because it deals with such large scale conflicts all the time, anything less than that in the game starts to feel very dull. The powers don't FEEL as satisfying as they do in inFamous. When I throw a car in Prototype, it doesn't feel as hefty as it does when you throw a car in inFamous with a shockwave. Things just feel heavier, weighter, and more realistic in inFamous. Cutting people up doesn't feel like you are cutting them up, just dispatching a baddie that drops some health for you. As I said, much more of an arcade feel. The attempts at stealth mechanics seem lacking. Sometimes, I feel like I am playing twister with the d-pad to do certain moves. (Hold R2 while pressing R1 and move the right stick to the tune of the macarena~! Okay, a bit of exagerration)
The Ugly: The game doesn't have the polish that inFamous does, but it's a multiplatform title, so that's not surprising (The game has to be catered to the LCD of the systems it is on, and not as much time can be spent on optimizing it for one system). The city looks dull, lifeless, and drab the entire game, it doesn't seem like an alive place like inFamous. Alex Mercer's character model is not as well done as Cole's in inFamous. What could be really cool morphing effects all use the same morphing-animation that covers the body while it changes. The character models, as a whole, are not as robust as inFamous (though there are ingame style cutscenes in Prototype, inFamous uses comic book style scenes to progress the story). The rocket launchers look silly.
Final Opinion: inFamous is a more polished game, graphically speaking. It has a much more comic-book superhero/supervillain vibe, as you realize you are a normal person with special powers. Prototype, you are something MORE than human, and aren't as constrained by human laws anymore. If you are looking for a gory superpower beat-em-up, then Prototype is that kind of game. If you want a bit more sandbox good/evil type game, than that would be inFamous. I'd probably give Infamous an 8.5, and Prototype like a 7 or 7.5
