Infamous is my favorite of the two, I own both and Infamous was longer and had more side mission variety, most of prototype's side missions were kill X amount of enemies in a certain way (with the exception of glide and running) Infamous's story was way better, prototypes story was revenge, and thats all. Infamous's climbing was more satisfying and made the city larger with 3 distinct side areas, while prototype you just kind of ran up walls, prototypes only differentiation between areas was Times square, and parks. Prototype had more different powers such as blade and hammerfist, and they all fell into a catagory like infamous. Prototype-Morphing, Infamous-Electricity. Infamous was better in graphics and had a lot of things put into the environment such as ability to suck electricity out of many things, and almost every ledge grabbable, and it was very easy to climb in Infamous, despite what others say you can climb onto places that you are trying fairly easily. I thought Prototypes idea of the web of intrigue was a cool idea but each little memory was too choppy for me, I felt it could have been implemented better. It was fun to consume people but there were only like 20 people to consume overall so there should have been a lot more unique people. Prototype has gore, infamous doesn't. I think I adressed about everything
ProtoType is supposed to be Infamous for the Xbox 360 (Not exactly, but you know what I mean.) So all it really depends on which console you like. Me i'm an Xbox 360 guy so, Prototype.
