Not having played Hulk, I'd say Prototype is the more unique one of the two. That being said, there are no side missions in the game, only time trials which weren't any fun. Even the story missions were highly repetitive. I did like few of the gameplay elements and Alex probably has cooler powers than Cole, but I also couldn't help but feel some of them were overused while most of them were underused or simply there for sake of artificial variety. Also for a game that uses so much melee, I'm quite puzzled by absence of standard hack and slash stuff like guard and counters (besides a couple of QTEs).
Infamous on the other hand, has best story missions. In fact I'd say if you ignore the side missions, you get almost excellent linear platforming/shooting mix with above avarage story and that's very difficult to top. Side missions too are actually fun of course. For example, I loved ring racing in Infamous despite my general dislike to that particular mechanics. In contrast the implementation in Prototype was quite possibly the worst I have ever seen.
Also in general Infamous cares for the player much more than Prototype; in mission checkpointing every second, cumulative experience even if you die, frequent missions to teach you your new powers, radar showing collectibles, etc. I died way less in Prototype, but it was much more frustrating experience overall, and I don't ever plan to touch that game again (already finished Infamous twice, including a hard run, all side missions and most of the collectibles). I also have to add, combat system and the few boss battles in Infamous are much more satisfying and fun, especially so on hard.
So yes, Infamous is the better game because it builds exceptionally well on its (maybe not so interesting) framework.