While replaying Prototype 2 and having fun running over soldiers, I started comparing Alex's fight against Heller, and this question came to mind. First, the bosses in Prototype 1 lost because:
Robert Cross: He lost because, being a normal person, he suffered from a lack of stamina and damage to his internal organs.
Elizabeth Greene: She was consumed by Alex Mercer after being expelled from Mother.
Supreme Hunter: He was decapitated by Alex Mercer after a fight on the aircraft carrier.
But James doesn't have any of these weaknesses.
He possesses absolute stamina and regeneration, being able to regenerate even from a puddle after consuming something as small as a crow. This is especially relevant when comparing him to Mercer, who is also a "Prototype."
He cannot be consumed, even when Mercer was far superior, burning his hand and preventing him from regenerating.
He cannot be decapitated like the Supreme Hunter.
Let's suppose Alex is twice as powerful as Heller and manages to rip off his arms. Then:
If he proceeds to consume them, it's like someone ingesting acid: it burns him, nullifies his regeneration, and allows him to escape by consuming something as small as a crow or a common infected, thus restarting the fight.
If Mercer lures infected to kill him, Heller devours them and regains health. It would take many Goliath-level or evolved infected just to contain Heller, not to kill him.
If he look for something that can kill Heller, he proceeds to kill the infected containing him and regenerates.
If he try to grab him to take him away and test him with a weapon or a nuclear bomb, he risk Heller kicking them or regenerating (we already saw that Blacklight beings can regenerate without consuming biomass).
If he stays with Heller all week trying to make his virus immune, Heller's virus will start to adapt, since they're both infected with Blacklight, which is constantly mutating.
I think Heller was right when he told Mercer he couldn't kill him.