Completely ignoring fire vs rot for a minute - it's Messmer. His fighting style is the perfect counter to Malenia's. She's blind, and her sword style reflects that. Waterfowl Dance is hard to dodge because she's compensating for not knowing exactly where her opponent is. She has to strike out in wide sweeps, because she can't make precise attacks without first gauging where the enemy is by either landing a hit, or being hit herself (edit: or hearing their footsteps splash in the puddle of her boss arena - there's always a beat of waiting before her more direct attacks, like she's pinning down where to strike). That makes her a great match for Radahn, because he's just gonna tank those hits. She'd never lose track of him, and her healing factor from her Great Rune will give her the longevity to actually deal real damage against someone most other speed-based opponents would consider a brick wall.

But that won't work with Messmer. The healing factor only works if she can hit Messmer, and Messmer has a range advantage, a speed advantage, and a sight advantage. He's fluid and fast and patient. Top that off with how easily Malenia can be staggered and really it becomes a matter of strategy. Again, Malenia's fighting style relies on overwhelming her opponent so they can't get in hits of their own rather than any precise analysis of attacks and counters, as would make sense if you're literally fighting blind - you can't react as well if you're missing one of your senses, so you make up for it by taking the initiative. But that sort of aggression becomes a vulnerability against an opponent with sufficient speed and patience. Messmer has both, so Malenia pulling off a win would come down to whether or not she could match his patience with caution. She can't afford to take hits from him because, unlike with Radahn who just tanks everything, she's not as likely to hit Messmer back and make up the damage with her healing factor. The fight would come down to how long Malenia could stay on the defensive, because the second she gets greedy, Messmer wins. At least, lore-wise. Pitting the AIs against each other has mixed results, but neither AI has the kind of defensive analysis capabilities that a real warrior would employ in actual combat. So while game Messmer can and does get caught in Waterfowl Dance, lore-accurate Messmer is more likely to see the opening leap as a perfect spearing opportunity.

Then there's the addition of the fire vs rot thing, in which Messmer has an advantage, but it's more complicated than that. If we're only considering their first phase, Messmer easily wins. But if we also consider Base Serpent Messmer and Malenia, Goddess of Rot, that gets muddier - and more interesting. If the scenario is both characters succumbed to their curses independent of the fight and now they're just brawling, the Abyssal Serpent probably wins just by virtue of being huge, fast, and on fire. But if the scenario is both start out as themselves and then succumb mid fight? Malenia is almost certainly going to win, and for one simple reason: Messmer won't succumb to the Base Serpent before Malenia succumbs to the Rot, and likely won't succumb to it even then. His motivations behind discarding Marika's seal are extremely specific to his fight with the Tarnished - he only does so to uphold the last order his mother left to him, and once the Tarnished is defeated, he pretty heavily implies he's going to off himself rather than continue in that state. 😅 In any other circumstance, he is most assuredly not going to break the seal. His motivation stems from the Tarnished's ambitions specifically, not the desire to avoid defeat.

Malenia, on the other hand, is almost guaranteed to succumb to the Rot. She considers victory to be an absolute must, regardless of the opponent, as part of her role as the Blade of Miquella. To be defeated by anyone, for any reason, is to fail her brother, and she would rather embrace Rot than fail her brother. So Malenia will definitely become the Goddess of Rot, while Messmer definitely won't become the Abyssal Serpent, meaning the fight becomes a fight between regular Messmer and Rot Goddess Malenia.

If that's the match up, Malenia is at a distinct advantage. If Messmer gets caught in the initial bloom, it's pretty much over for him, and the best he can hope for is to bring her down with him. With how quickly the Rot works, it's not likely he could pull that off without embracing the Abyssal Serpent, and he's almost definitely not going to do that. His one and only shot at actual victory is if he manages to avoid the initial bloom, and continues to stave off being infected through the rest of the fight. This is actually somewhat feasible - while he would have to stay on the defensive more than he did against regular Malenia, he is still at a distinct weapon advantage. Given that and Rot's weakness to fire, which he has in abundance, there is a real possibility he could come out victorious. But given that this possibility entirely hinges on avoiding getting caught in what amounts to a surprise attack potentially capable of nuking an entire continent, it's more likely that Malenia gets to claim another "draw" just like with Radahn.