I think is was a mistake what they did with Alex in prototype 2, his fate should've either been left ambiguous or he should've been helping Heller deal with his power and goals in some way (powers acquired through different means than just 'mercer infected him')
And the villain should've also been someone else (not PARIAH, that seems too easy)
The way I see it the reason why Mercer lost is because he had nothing to fight for no motivation or cause except finding out who he was and keeping people at a distance which is the reason why he had a blank stoic face and no emotion whatsoever and never letting get close to him whereas Heller on the other hand had a cause which was finding and saving his daughter Maya and avenging his wife Colette also with having emotions and letting people get close to him making more human than Mercer ever was as a scientist and as a virus. The way the writers wrote the first game really fucked up big time with Alex making come more as a villain rather than a full fledged anti-hero that James seems to fit better cause he cares about innocent people. If Alex does come back it has to be from scratch and one with a sense of morals and human guidelines but without all of his powers and protecting innocent people from criminal scumbags and crime organizations and a new virus that makes him an anti-hero full force along with making look like a badass character but having no memory of his past and not the fucked up emo shit stain in P1 or the piece of shit megalomaniac in P2.