I never played the original, was Nemesis really Mr. X from RE2 but mutated?
Mr.X is a T-103, mass produced Tyrant made by Umbrella. It's just one of many.
Nemesis is a T-103 infected by an experimental parasite named NE-a Type.
So it's not the same guy from RE2, it's another one. The parasite is the reason why is face is so fucked up, it's tearing through its skin.