I recently played both Prototypes for the first time back-to-back, starting with Prototype 2. The protagonists in both are incredibly unlikable and the plots were downright terrible. That said, from a gameplay perspective, I found Prototype 2 sold the power fantasy of a shape shifting, tentacle monstrosity in a much more satisfying way. Prototype 2 scales nicely, you start the game being able to leap tall buildings and wreck a few things with your powers and by the end you're soaring above city blocks, running around as fast as The Flash and eviscerating everything in sight. I found with the first Prototype, the further I got in the game the more I had to rely on vehicles and weapons, not your fantastic powers. I found the design of the first game to be downright lazy and arbitrary. You killed stuff, earned points and just bought powers from a menu, there was no context for any of it in the game itself. In Prototype 2, you kill an enemy with a new power, absorb that power Mega Man style and immediately have to use it against specific enemy types. Even the upgrade system for your power was tied to openworld activities, you see a beasty with a genetic marker over top its head and drop what you're doing to stop, fight, kill and absorb it for an upgrade.
I had fun with Prototype 2.