i think it's an excellent idea. you get to play a new character instead of the same old character. change is good. if you dont like it dont buy it. but i know i will enjoy it as much as the first one so more fun for me!
Since Prototype is one of my all-time favorite games, I've been scarfing down every little detail I can find on the next game. If it makes you feel any better, the devs said that it's possible that it's not the real Alex Mercer that infected James Heller with Blacklight. The second game does take place a year and two months after the first game's ending. Frankly, I KNOW there's more going on behind the scenes than Heller's simple grudge against Alex. There's a bigger picture here we haven't seen yet.
Let's hope this one is properly polished. The first game felt only half finished and the plot was very poorly executed. It had a very cool sense of speed with running up buildings/jumping but not much else going for it.