LOL! Snake may be straight, but he's still a perv!
Seriousness makes it weird, tone needs altering
It started off with potential for appealing to the more perverse side of our sense of humour :) but I think the poignant mood of the music and Snake getting all depressed for comic effect jarred with the perverse humour too much. It just didn't fit and it felt more creepy than funny from that point on.
Maybe it would have worked better if he gets angry or frustrated instead.
I did find Otacon's role funny at the end, as there's always alot of jokes about how far bromance can go before it is officially awkward, especially with these two. However his part needs to be less serious too, maybe suddenly appearing, breaking into super fast flowery dialogue about love like some kind of fangirl possessed. Anything to make it a bit more ridiculous and move away from the lonely atmosphere.
No idea if any of that would work better, they're just some of my thoughts. If you insist on using codec screens with little or no movement, your script has to be really good to stand up on its own.
SNAKE GOT PWNED BY MAI LING
"I understand you snake"