I think Captain Falcon has more sexual encounters than Commando so I would say in a battle Captain Falcon would win as he'd be able to seduce Commando faster and be the top. The man's a bounty hunter he probably meets all sorts of weird alien chicks and dudes he gets freaky with. All Commando does is like be some sort of future cop? But he also plays the guitar on sidewalks for money so it's clear he's broke as shit, probably doesn't get around often and no one wants a broke bitch. I don't think he'd be really able to compete with Falcon's experience or his girth. Cause I'm pretty sure u need some sort of big dick energy to be so strong that you can summon a fucking fire bird out of sheer will, Commando has to rely on his shitty gadgets to even get a stream of fire, which is also fucked since that's banned in the geneva conventions. Falcon can get away with it though since he's not from earth and it looks cooler, i'm pretty sure most people can turn a blind eye when they see a fucking fire bird come out and his ass when he does that pose, with commando though he just burns the guy and you just hear and smell the guy suffering, that's not really heroic.
and its a shame we'll never see this crossover happen in real life because cosplayers for these two are rare but also the companies don't seem to know what to do with them. capcom stopped outsourcing after the failures of DmC and Dead Rising 4 so we're probably never going to see another captain commando since only smaller outsourced projects were capable of that as in house capcom is busy on things like REmake 2 and DMC5 and the captain was already obscure at that point so chances are we're never gonna see him again, ever. and that's great.
and with captain falcon, much like how prime minister abe isn't doing much to improve the declining birth rate in Japan, Shigeru Miyamoto isn't doing much with the f-zero franchise and he seems to be stuck on this idea that games need to have some dumb gimmick to play with and since he's too old to come up with something then chances are we won't see another f-zero game, not until he croaks anyway, which is sad because all the imitators just fail to live up to F-zeros' creative tracks, music, and characters. so i think as far this battle there's no clear winner, just losers who sadly never caught on with the mainline gaming scene and are more popular as obscure choices for popular crossover fighting games.