I don't really get your beefs with the combat and controls, I found them entirely responsive and pretty easy to use. In fact the high point of prototype 2 is it's combat in my opinion. It's fun, quick, you have a bunch of options for weapons that are all around pretty well balanced, unlike prototype 1 where once you got the whipfist everything else sucked. Whipfist still wins at crowd control, admittedly, but it's not quite the game breaker it used to be.
That said, the story is shit. The villains are utterly laughable in how flagrantly evil they are. I believe I mentioned this in another thread, but there are sections where you see flashbacks of a soldier complaining about killing zombies because he wanted to kill people instead. His commander, instead of writing him up as psychotic and unfit for duty, basically tells him "I like your attitude son, you're gonna go far." The radio chatter is also similarly psychotic crap about them being happy to kill civilians and otherwise going out of their way to scream "Have I mentioned that I am DISTILLED EVIL today? I haven't?! To the orphanage then! Where we shall conduct brutal experiments in between bouts of baby maiming!" And that's not even the main villain either...
The characters were one dimensional, they took the interesting sentient virus concept and buried it, they reduced the chance to have more complex discussions between the soldiers to have spout "nurr hurr hurr evil" at every opportunity, and they really give no adequate reason as to why the hell mercer infected the protagonist in the first place. Mercers plan would have worked perfectly, but I guess he felt that was too easy and gave himself a tailor made "dude to destroy all my plans." Hell, that could have been an interesting discussion, maybe Mercer deep down had doubts and that's why he made Heller. But no, no intelligent character discussion allowed.
All that said, I would play Prototype 2 again, if only for the fun of hulk smashing my way through legions of soldiers, tanks, and choppers.