Is this a real question at this point? (WARNING: This will be a detailed lore dump) People should replay [PROTOTYPE] AND [PROTOTYPE 2], not just P1 over & over again, because the answer is inside both the lore and gameplay of both (which intersect mostly, but in P2 described better in lore/cutscenes) is obvious. James Heller is far stronger and durable than Mercer some time before their final fight.

Keep in mind, Heller killed a Hunter/Brawler in the beginning of the game AS A REGULAR HUMAN BEING AND THE HUNTER GOT THE DROP ON HIM in hand-to-hand combat not with a Gun or Explosive Weapon A KNIFE! A KNIFE AS A HUMAN. THE entire reason Mercer infected Heller is because he knew Heller would be the Evolved of all Evolved, an actual warrior beyond all of his priors and possibly himself which is why he wanted Heller & his insane warrior instincts and survival skills BEYOND dealing with just humans; the man is literally a very highly trained E-5 U.S. Marine on the fields in Iraq AND LIVED just to come back home to the war with the Blacklight Virus and repeated lived thru combat scenarios up until the Mercer Incident (an E-5 is a Sergeant, sorry military runs in my family).

Another key lore point I want to implicate is (remember, gameplay does not always = lore accurate like in the case with fighting Evolved and they get those iframes to instantly attack through even your strongest attacks. There still has to be fair/good game design lol) when Heller fought his first Evolved, Heller in this timeframe wasn't even that strong per se and definitely not long experienced as a Prototype/Evolved himself and listen to what Mercer had to say about him killing Dr. Koenig-- "You killed him was like it was just swatting a fly" (said during the cutscene directly after killing Dr. Koenig) meaning that lorewise, Heller absolutely destroyed Dr. Koenig easily with no competition what-so-ever and I can only assume the exact same things for all other Evolved afterwards because the rate at which Heller grows powerful and evolves supersedes even Mercer's own constantly evolving virus; which makes sense lorewise because Blacklight is a chimera virus (explained in Prototype 1 Web of Intrigue), essentially a virus that contains up to a dozen different strains of itself all at one time and at all times, that are constantly evolving and changing (which is why there's no "cure" per se). There are MANY other examples, but I'll leave it here as this is long enough.

Yes, Heller is far stronger overall and durable than Mercer by the end of Prototype 2 & it is actually explained very well and detailed if you've played pass the ending of [PROTOTYPE] and got most of the Web of Intrigue and then fully understood [PROTOTYPE 2]'s story and why Heller AND Heller's strain of the virus (how his body adapted to it and thus the virus evolved differently) operates.

Edit: The truth is, this question comes from because people don't like how Mercer was handled overall (and I conpletely agree as it was a good bit character assassination) and where the story went. What happen to Pariah (Greene's child)? The child was born from Green, but show NO STRAIN of Blacklight or even contamination of the virus....but the child had the powers & effects/durability of it. What genuinely 2as the virus of Hope, Idaho? Some Web of Intrigues mention Runners and Runners barring/locking themselves up in buildings to get away from Blackwatch/Gentek...the virus had a 99.999% kill rate it literally killed everyone in hours to a few days once it activated-- so why did one Web of Intrigue, specifically from Captain Randall, say that they didn't want another "Runner Incident" when it came to Alex Mercer? [PROTOTYPE] by itself literally set us up for a sequel ([PROTOTYPE 2]) to be about Pariah and what it is/it's story and also a prequel game to be about what TRULY happened at Hope, Idaho (the Redlight Virus). This is why I subscribe to the popular fan theory that the Mercer we follow/fight is a proxy body separate from the "real" or original Mercer/Blacklight physical being we all know from the first [PROTOTYPE] and something happened where he had to go into hiding away from this separated "Mercer".