I bought inFamous and a friend bought Prototype. We beat our respective games and then traded.
Free roaming is TONS better in Prototype. TONS. Getting around the city is just much more fun than in inFamous.
The story is better in inFamous. I'm about 2/3 through Prototype, so my opinion could change, but so far I'm not caring at all about Alex's plight.
Causing generic carnage is way better in Prototype as well. Penny Arcade says you can KARATE KICK A HELICOPTER. Well, I'll follow that up with YOU CAN ELBOW DROP ON A TANK. Widespread destruction is easier, and more fun in Prototype.