A vast improvement over the original.
I'm going to get this out of the way first: Yes, Alex Mercer isn't the protagonist. Yes, some people call "character derailment". If it really bothers you, pretend he's a clone or something and try not to let it ruin your enjoyment of what is otherwise a fantastic game.
They took everything that made Prototype less than perfect, and they fixed it. The graphics, a serious weakness of the first game, are absolutely stellar (although they're designed for HDTV, and if you don't have one, some areas will seem a little murky). The range of enemy types is broader - there are twice as many types of Infected - and while Heller doesn't have any more powers than Mercer did, every power he has remains useful throughout the game. While the optimum strategy with Mercer was often to steal a military weapon or run around throwing cars, with Heller you'll want to get up close and personal to use your powers. The side-missions aren't exactly "integrated into the story", but they do at least make sense for Heller to be doing, and they're fun rather than medal-chasing.
You might have seen the trailer for the Hunting power - if not, look it up - but you really do have to use it to understand just how amazing it feels. There's nothing like picking your target out of a crowded boulevard, dropping on them from a hundred feet up, and eating them alive to make you feel like an unstoppable monster (oh, that's another thing - the targeting of the grab attack has been VASTLY improved. Consuming people mid-fight or picking up stuff to throw is no longer a crap shoot).
Unlike the original, this game has a strong thread of humour. Several moments are genuinely and intentionally funny, and while the overall situation is just as nightmarish as the original, the game itself is nowhere near as unrelentingly dark.
As for negative points: The camera can get a bit screwy at times, but no more so than in the first game. A lot of the backstory exposition and conspiracy-theory plot from the first game is missing, which is a shame. The game is definitely easier than the original (although it does have an unlockable Insane Difficulty). You can't choose when to buy new power boosts - you're forced to whenever you level up.
Finally, there is a LOT of swearing in this game. You don't want to play this with young kids in the room unless you want to expand their vocabulary.