Okay, sorry for taking a couple of hours, but I am busy with University (and I still am at my University, I'm typing this in my break right now), so... Yeah. Anyways:
1. It was elaborated in
this thread. Basically, the main reasons why Mercer's Regenerationn is listed as "Mid-High" is because we literally see a last second scene of Mercer getting incinerated from the inside and out by the nuclear explosion, and thus Occam's razor says that he got vapourised by the nuclear fireball. Given that we have evidences that nuclear explosions has incinerated people to ashes or even vapourised them in real life, Mercer surviving by regenerating from such is an explanation that requires the least amount of speculation, especially when we literally see yellow fiery light emitting out of the orifices of Mercer's body (and other parts of his body) when the nuclear fireball reached him (which proves that the nuclear fireball was actually incinerating him to extreme levels).
Also, keep in mind that there is a timeframe between the nuclear explosion detonating, and that time when Mercer's biomass was on the shore. Given that we see an instance of Mercer getting incinerated, we have determined that it is most likely that he was recovering from that purely by Regenerationn, and that the biomass we've seen from him is what he has actually managed to regenerated so far (rather than "what is left over"). The only problem is that we don't know the exact timeframe between those scenes, so we assumed that is a few hours based on the nuclear detonation scene happening at night, and the recovery happening at night (probably indistinguishable from the time of the nuclear detonation). Now, for your points.
- There is no explicit evidence that says that Mercer would "never be able to recover" without the crow. If anything, there are evidences that says that he would've been able to recover without the crow, but how much longer is unquantifiable. Such as this scene, where he was able to reform that huge hole in his head without needing to consume anything. Or Mercer scaling to the Supreme Hunter reforming a hand from a puddle within just a couple of seconds without needing to consume anything at all (thus, it is most likely that the Supreme Hunter reformed the rest of their body at a similar timeframe to when they reformed their hand). Keep in mind that the Supreme Hunter is a being designed from Alex Mercer's own DNA, and has noticeably inherited abilities from Alex Mercer to prove such (such as when the second fight with the Supreme Hunter shows him performing a Devastator, and we know that Mercer is the only other character who can perform Devastators in Prototype 1). If the Supreme Hunter can do it, then so can Mercer as he is the one that the Supreme Hunter inherited their abilities from. And even then, Mercer has to regenerate from far worse circumstances than the Supreme Hunter ever did, such as the sheer damage the nuclear fireball did to him.
In fact, even the Health Regenerationn upgrades supports the characters having Regenerationn without needing to consume for biomass, such as the mechanics in Prototype 2:
Regenerationn
==
Enhances Heller's ability to get health back without the need to eat people.
Level 1: Health bar regenerates up to 50% outside combat. Better than it sounds, since this Regenerationn is nearly instant. This saves a lot of wasted time wandering around eating people, and might also help ease your conscience.
Level 2: +30% health from consuming things. This is GREAT. The best way to survive in a lot of fights is to consume people.
Level 3: Health bar regenerates up to 100% outside combat.
Level 4: Health bar slowly regenerates even in combat. The Regenerationn is painfully slow and will rarely make a difference.
However, the inside and outside combat mechanic is likely assumed to be the limitation of Game Mechanics (especially when Prototype is one of the rare series where game mechanics makes them seem weaker than they are portrayed to be lore-wise, when compared to other series where game mechanics makes characters seem stronger than they are portrayed to be lore-wise), but I digress. Also, do note that Gameplay mechanics are allowed to be used for video game characters in this site, just as long as it doesn't contradict the characters' established capabilities.
Source.
If anything, the evidences we find suggests that the Regenerationn of Blacklight characters doesn't depend on biomass (so they can still regenerate without biomass). At best, evidence suggests that biomass only boosts the speed of the Regenerationn and nothing more. And even then, the Blacklight characters' ability to regenerate without biomass should be pretty quick if the best damage inflicted only reduces them to a puddle (rather than vapourisarion), as the Supreme Hunter was able to reform from a puddle within several seconds.
Based on what consistent evidences we have gathered, biomass would only make the process faster, and not actually be the source of the Regenerationn like you're thinking of.
- The reason why that fight is considered as PIS is not the fact that Heller defeated Mercer, but it's the fact that Mercer's Regenerationn should've been able to reform from the loss of said limbs. In fact, he did so several times, and yet he all of the sudde didn't in that one last moment. Given that we see Heller being able to gain enough of armless Mercer's biomass to be able to unleash tendrils that surrounded an entire city, Mercer should've been able to reform an another set of arms.
- Think about it. Even if we somehow assume that Blacklight characters can only regenerate with biomass (which it isn't), Mercer should've had more than enough biomass to reform an another set of limbs. If a crow is all it took to give him the boost needed to recover in Prototype 1 in such little state of biomass that Mercer is in, then a city-wide biomass should've been much more than it is ever needed to reform some mere limbs. The only likely explanation is that Mercer not reforming those arms are nothing but PIS that shouldn't apply to his true capabilities, especially when we saw him reform such several times, and I wouldn't even be surprised if the reason Heller won is because he's "the protagonist" compared to Mercer being "the antagonist". Given that Heller was able to resist Mercer's Biological Manipulation as a result of "Resilient DNA" (and not having any further explanation about that), this is likely just an another of the many plot holes of the flawed game that is Prototype 2 in regards to Mercer's Regenerationn.
- You do know that at that point in time, Mercer still thought he was human, right?
- He thought that he was a human early on, and and that he should be restricted to the same limitations as humans are. Yet, we see instances of Mercer being incredibly surprised when he performed superhuman feats. In fact, the "wounds" that early-game Mercer had on him didn't even inhibit him in any way despite his reactions to it (which links to how he thought he is a human and being restricted like one). And yet, when that Blackwatch soldier shot him in the head, he just got back up and body-dropped that soldier as if the damage he sustained are nonexistent. Given that Mercer is a shapeshifter that has control over his entire body at the genetic level, it is likely that Mercer has control over the speed of his Regenerationn as well (it would definitely explain why he didn't reform that huge hole in his head when disguised as that soldier, and yet he reformed that hole when he stood back up in the span of around a second or two. Given that he has control over his density as well, it could also explain how a bullet from Randall even harmed him in his disguise, as he probably lowered his durability into an ordinary human's in order to blend in).
Nobody is saying that Mercer's Regenerationn is limitless, just that he can regenerate without needing biomass (with biomass speeding up the process, but nothing more), and that we don't know the limits to it (thus, it is unknown to us, so we can't truly assume what the limits of it is).
The "limit" you're talking about involves PIS (that final scene with Heller vs Mercer), when all the consistent evidence we have gathered says that isn't the limit you're saying it is. Even the nuke scene doesn't prove that the Regenerationn of Blacklight characters are entirely limited by biomass, just that "it is not at all dependent on biomass, but biomass can increase the regenerative speed".
2. Regenerationn and Stamina are not treated in the same category. They are treated differently, especially as far as fiction goes. There are fictional characters whose Regenerationn doesn't have any known limit, yet we see such characters showing signs of physical fatigue. There are even some fictional characters whose stamina doesn't have any known limit, yet their Regenerationn has shown to have limits in some way. In fact, the reasons why Mercer's stamina is limitless is because:
1) He has never shown to physically tire out in Prototype 1, despite all the physical activities he's been through.
2) His abnormal physiology as a sapient virus (not a human) says that he doesn't operate in the same way as humans do. Especially considering that he is a shapeshifter with control over his entire body at the genetic level.
3) He can function without needing his internal organs intact (such as when he was able to move around when the huge hole in his head should've rendered his brain into mush). If he can operate without needing internal organs, he should not be able to conventionally tire out at all. Period.
There might be more to it, but that's the answers I have to your points at the top of my head.