I wouldn't call that racist, but that is totally inane. First off the character isn't exactly a black guy he's not even human anymore, also he's a shape shifter you are not stuck as a black guy. I don't know how you can be immersed as playing a white mutant but not a black one it just seems laughable. I mean it's like would you have any trouble playing a super buff muscular looking character guy in Elder Scrolls if you were over weight in real life?
I don't know how it works in Prototype 2, but in the first one you'd shift out of your disguise as soon as you used a power, so that wouldn't be very useful. And it's not about what I look like in real life, it's what I'd
want to look like. Though, without boasting too much, I don't look too bad myself.

Still, from what I'm reading about the gameplay here, I wouldn't enjoy Prototype 2 if James Heller looked like Hugh Jackman. While I enjoyed Prototype immensely, the gameplay wasn't exactly very complex. Dumbing it down sounds like a horrible idea.