thought I'd give my own 2 cents.
location-I love running around NYC but it doesn't feel real. the textures feel pasted on and overly shiny. Infamous, on the other hand, has a city that really feels alive, with every detail beautifully crafted and well thought out.
movement-so much more fun in prototype. all the climbing and jumping in infamous gets old really fast
bosses-goes to infamous. the bosses weren't hard but they were very interesting. prototypes boss battles didn't give any sense of acomplishment and the final boss is a pain until you know the trick and then its painfully easy.
graphics- infamous looks nice but there are moments when the animation feels way off. some of the running animations. but in prototype the camera can cut through the models in cutscenes and that looks aweful. infamous has style, prototype has realism.
final feelings-finishing prototype left me with a hollow feeling in my gut. the final boss feels like they couldn't find anything better. they should have had more battles with the hunter, some plot hook to make it really really important to kill him. he feels so cookie-cutter. you have to beat him because he's in the way,they could have filled that role with anything, even a tank or a bunch of soldiers. The should kept the specialist human and have him turn on you or keep Elizabeth as the running villain. she had so much developmental charater.
I loved the moral system of imfamous and I cose the evil ending. I go through all the trouble and for what? a little MUHAHA. sheesh!! have him hook up with sasha, have us choose whether we kill her, free her or seduce her. the army is getting ready to take back the raysphere they think is still intact and so you do what? run around the city after the final scene doing those quests. let me consolidate my power, send the world a message that I control this city. I wanted to control the reavers. there could have been a whole nother part of the game. but nooooo. what really stings is that I'm every one's worst nightmare and the next game will probably start with me running to a new city and starting over.
also a note:DESTRUCTIBLE BUILDINGS: its not any fun when every explosion looks the same. its even less fun when its like it never happened after 5 min. Even just 2 explosion animations would have been enough. and have a few buildings stay ruined! they went through the trouble of painting a hole on geneteks roof after you know what. so why not pick like one hive and one base that stay ruined the whole game? and whats with disappearing gore? blood is gone in like 5 min. that is so silly. have the gore stay for a real time day or two. You could paint whole buildings.
which reminds me : WHY Prototype WHY can't I aim manually? just give me a view finder like infamous. seriously. I want to paint a wall red for the heck of it.
Also later in the game all soldiers should alert when they see normal alex. would make things much more stealth based. And have a few more enemy types.