I don't know why the OP is so insistent on concluding this matchup when even Death Battle themselves treated this matchup as a crappy-tier matchup, but fine, I'll provide my own points for this matchup:
With speed being equalised, Mercer likely haxstomps. One could argue that Cole stomps instead, but that also proves this matchup wasn't fair in the first place, since either could stomp.
Of course, the one major thing that hasn’t been brought up yet is the Blacklight Virus, it has a lot of stuff to cover and is Alex’s most prominent wincon, having hundreds of strains, being capable of driving people mad, and its general potency as a virus is almost unmatched, so how can Cole handle it?
Well for starters, thanks to being able to fend off Sasha’s tar, which is a mind control agent that can drive people mad, the mind and madness aspect of the Blacklight Virus would fail to mess with Cole. Furthermore, considering Alex’s main method of trying to infect Cole would be the gas he can release from his body, the most obvious and blunt answer would be Cole to use Ionic Vortex to… literally blow it away with a tornado-it has mass, it’s a gas, it can be tossed around by high winds such as a tornado to prevent it from getting close to Cole.
But if Cole were to get infected, there’s a shockingly hard counter to the Blacklight virus being able to survive in Cole's body. Most viruses die within the mid-100 degrees Fahrenheit or so, and while Alex did survive the nuclear explosion, the distance means the heat he withstood wasn’t as much as it could’ve been meaning the Blacklight Virus’ heat resistance isn’t too potent. Why does this matter? Because Cole's lightning, which is generated passively by his body and can surround him in a storm of electricity, gets up to 50,000 degrees Fahrenheit, far hotter than anything the Blacklight Virus would have survived, meaning it’s a genuine possibility that Cole could literally fry the virus out of his body even if it were to enter him, preventing it from infecting him at all.
Cole may have fended off Sasha's tar (with great effort, and even then he was shown to suffer symptoms from it), but his struggle with Sasha's tar proved one thing - Cole's electricity was
not able to fry Sasha's tar or the disease it inflicted him with away from him.
And nowhere was it explicitly stated that Sasha's tar has resistance to heat by itself - Cole could've just fried the disease from Sasha's tar the moment it entered his body, but he was unable to... I don't know about you, but that heavily implies one thing: Cole might be able to
from electricity from his body, and he could absorb electricity into himself, but his electricity does
not appear to be outputted from every cell in his body or otherwise.
That point about Cole's lightning being generated from his body would need
explicit statements/scans to prove that every single one of Cole's cells generate electricity - and Cole being susceptible to Sasha's tar (and its disease) previously is pretty much an anti-feat that doesn't really help support Cole's electricity coming out from every single one of his cells. So unless Cole generates lightning-level electricity from every single cell/molecule from his body, the Blacklight Virus would only need access to one of Cole's cells before it rapidly self-reproduces and overtakes Cole's body (with Cole being unable to fry it out of his body like how he was unable to with Sasha's tar) - it doesn't matter if some of the gasses didn't go through, Mercer would only need a sliver of such gasses to get exposed to Cole for the Blacklight virions to infect Cole.
Though even if Cole decides to fry the Blacklight Virus, and Mercer, they would just regenerate anyways, due to Mid-High Regeneration - and via scaling to the Supreme Hunter's feat, Mercer would just regenerate under 24 hours (since the Supreme Hunter could even reform a hand within seconds while being a puddle without absorbing anything or having any excess biomass to boost his regeneration speed), so Cole would not be able to incapacitate him just by nuking him with higher AP alone.
For Cole using Ionic Vortex, there would need to be explicit scans to prove that Cole has used Ionic Vortex against gasses in-character. I have yet to see a scan provided where Cole uses Ionic Vortex to drain up gasses - and even then, Cole would need to do it forever, which he can't because he would need infinite stamina (and Karmic Overload is temporary), so Cole would run out of energy and then Mercer could use that opportunity to gas Cole again before Cole could get the chance to absorb electricity from his environment... Though if this is RFI-empowered Cole (which I don't think the OP has specified for Good Cole. I don't know why RFI-empowered Cole should be used since I don't think even Death Battle decided to use RFI-empowered Cole, but whatever), stamina would not be much of an issue for Cole, but he would need explicit scans to show that he uses Ionic Vortex to suck up gasses.
So, showcase explicit scans where Cole's electricity is able to be generated from every single one of Cole's own cells/molecules, or else that isn't enough to protect Cole from the Blacklight Virus given that Cole's electricity also didn't protect him from Sasha's tar (with inferior feats to the Blacklight Virus).
"its not really in character for Alex to use the Blacklight gas as his primary combat option."
Yes it is.
Mercer uses gasses even against ordinary humans at Penn Station, and he used gasses with the infected Whitelight against ordinary civilians to infect them.
Mercer
hates humans as of, and the entire point of Prototype 2 was that Mercer wanted to infect all of humanity - so Mercer not using gasses against non-infected, like Cole, does not make sense when that's literally the only instance we see how Mercer dealt with non-infected humans that isn't James Heller (who is protected by plot armour). He didn't use gasses against Blacklight James Heller or any other Infected because they were already infected with the Blacklight Virus, so no point in trying to infect what's already infected after all. XD
Also, electricity won't really paralyze Mercer if he decided to get his Shield ability out, as his Shield ability was able to prevent electricity from affecting him like in Robert Cross' fight, so hardened biomass (such as Mercer's Shield or even his Armour form) would be able to prevent Mercer from being paralyzed. It admittedly won't help Mercer against the huge AP gap between him and Cole, but paralysis from Electricity actually isn't much of an issue if Mercer decides to harden his biomass.
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Though if others decided to argue that it is a stomp for Cole... Then this matchup should never be added in the first place, shouldn't it?
If a matchup is a stomp, then votes are all invalidated anyways, so votes don't matter if a match is a stomp on VSBW. ^_^;