I bought Prototype today (or yesterday, whatever) and it's a lot of fun. Reminds me of Spider-Man Web of Shadows mixed with Hulk UD.
While infamous and prototype do play very different, it's really eerie how similar parts of the games are. It's even more similar to Web of Shadows.
The origin of both characters is waking up with powers while others are infected. The city is quarantined off by a military force. The one escape is a bridge, which is covered by mounted turrets. Each "level" or set of missions starts out with saying what day of the infection it is (Infamous starts in the late teens, Prototype at Day 1).
For Web of Shadows, both take place in New York. Both games show the spread of the infection as the game progresses, usually with buildings covered in the infection and areas with those infected roaming around. The infected monsters you fight have almost the exact same design. The wall run mechanic is largely the same. You have a wipe attack in Prototype that has all the moves the Black Suit had in WoS. There is a charge attack move in both games where you summon giant blades to come out of the ground (both games even have the range depending on how long you hold Y).