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Full agreement. Prototype 2 broke my heart.

Yeah, he was made a total edge boy with no real sense. In Prototype he was at least a very cool and interesting edge boy.

It was just a complete turnaround from the first game's character arc. I'm not saying Mercer was ever a good guy, because he's not even close, but what they turned him into in P2 was more like the human Alex Mercer - which is someone the virus Alex utterly despised. His reasons for turning evil were just flat-out stupid and felt disconnected from the original game, wherein he was gradually gaining a conscience.

I've somewhat made my peace with the game - I've talked to Dan Jolley about why they did that, and it turns out he's a pretty great guy even if I'm not the biggest fan of his writing. And since the two games were produced by entirely different teams, I have an easier time pretending the second doesn't exist.

Yeah, I agree. The turnaround was extremely random,it might've not been Dan's mistake ( after all writing needs to be approved by the devs ) or he just had an entirely different vision and someone wanted Mercer in it. Anyhow, the sudden change made little to no sense and Mercer being the supposed "villan" could've been handled better, like for example him being blamed despite, say, no intention to spread virus again.

Of course there's an option ( from what you said a likely one ) that Dan just wrote what he wanted to do. But yeah, both games were made by different teams, though I, for one, pretend that Prototype 2 is just a different, spin-off game and simply praise the somewhat improved gameplay.

Well, Dennis Detwiller was the lead writer of the first game and Dan Jolley was the lead of the second (and both were, of course, devs.) However, the executive decision to make Alex evil was handed down from a different department - Jolley was just working within the parameters he was given, which were to make Mercer as evil as possible and Heller as good as possible. So I can't blame him there.

Having said that, I vastly prefer Detwiller's approach. Prototype as a setting was never supposed to be straight heroes and villains, which P2 simplified it down to. Nobody was completely evil and nobody was completely (or even close to) good. Even the zombie apocalypse broodmother was just a pitiable victim, in the end.