Since he became such an ass, don't really mind killing Alex Mercer... but I find it rather puzzling:
1) if he wants to wipe out the population, why save it in P1 from the nuclear weapon?
2) he seemed to have retained some of his humanity in P1 (saved the people from nuclear detonation, asked that doc to take care of Dana). why did his ego evolved into this SOB in P2?
3) upper Manhatten was detonated in P2 ("death zone"). WTF!?
4) at the end of P1, something regenerated from the bloody mess Alex beat up. What was that and what became of it!?