Welp, for starters, neither of them is going to be possessing/infecting/absorbing each other anytime soon.
Alex's resistance to Mind Manipulation is actually a legit hard-counter for Carnage's mindhax. (Being that the latter is based on Carnage forcing his own thoughts into the minds of his victims)
Alex's regen is technically better, but functionally, they're both the same in that they don't really have a means of physically stopping each other from regenerating.
Both have fought extremely similar enemies. Alex has done so in the form of fighting his fellow Evolved, while Carnage has done so in the form of fighting other Symbiotes. (As well as Spider-Man, who is at least as intelligent as Mercer if not more so)
Alex technically has better mobility (via gliding), but Carnage's own mobility options are more reliable.
Carnage can see out of every bit of his Symbiote, meaning he has far better awareness of his surroundings here.
Physically speaking, Carnage is far stronger than Alex. Not only is his lifting strength much higher (Class M VS Class K), but checking
here tells us that Spider-Man alone sits at 1.271 KT, only slightly weaker than Alex. Carnage dwarfs Spider-Man in the strength department by leaps and bounds.
Leaning towards inconclusive, actually. It's almost a mirror-match, and what few advantages the two characters have are minor at best. I don't really see either of them defeating the other's regen for good either, and while Cletus could go for the incapacitation by trapping Alex within his webbing, that's not something he does in-character.