Prototype > Hulk as well. I've yet to play Prototype 2 though.
Unfortunately I was waiting for someone to mention this so I could disagree.
There were a ton of features present in Ultimate Destruction that were absent from Prototype. Gameplay nuances, really.
The power wheel of Prototype is cool, but it just felt like ripping Hulk apart into seperate forms. Hulk still felt like he had more options at his disposal. The Claws in Prototype are only usable for the first hour or so, then they should never be selected again unless required for a challenge. Most of the challenges in Prototype weren't as creative or fun as Hulk's.
Hulk's weaponization of his environment helped create depth to the world around him.
Lack of actual cheats in Prototype seriously killed replay, as did ripping out co-op (which was initially my biggest draw to the game - Hulk but now double trouble.) I wanted low gravity, rainbow blood, bottle rocket bullets, cars that would burst into confetti when they crashed, thermobaric tanks that would scream "hallelujah" every time it was shot. Shit like that as cheats, not one early unlock ability, which fucking sucked anyway.
Though, the parkour movement of Alex Mercer was very cool.
Prototype was almost equivalent to Hulk: UD, which by its own right is an achievement. But, Hulk gave me compassionate options as well as destructive. Being able to place an accidentally grabbed civilian down, only to pat them on the head was cool, but I could also just set them down, and fucking flick them into the horizon like a tiny tick. Granted, Prototype was going for balls-out violence, but at least give me more versatility with my abilities along that violent path.
My contribution to the topic at hand though:
http://www.giantbomb.com/spiritual-successor/92-425/
Personally,
Vanquish > P.N.03
Fallout > Wasteland
No More Heroes > Killer 7