Throat slitting is a move you get only for reaching level 3 in CQC.
The CQC has some real benefits to those who use it. Keep in mind CQC isn't a frontline combat thing. Instead, it's for people who sneak around. If you try CQC in frontline combat whatever enemy you get in CQC will just have his teammates shoot you in the head while you've got him grappled.
However, if you sneak around and find guys on their own, you can take them out of the action longer than if you'd just killed them.
After putting someone to sleep it takes a long time for them to get up unless a teammate is nearby to wake them up.
Also, the game spawns random boxes (it should probably spawn random drums too), this was one of the best ideas of the game. The boxes aren't too common, but they're common enough that players won't check every one, especially if they're in a fight.
There's actually a lot of room for MGO to expand, especially in the area of adding in more support skills. I'd love to have some kind of medic skill as there's no way to heal in the game. I'd be fine if the skill took up 2-4 slots at level 1 so long as it was useful.
Same for things like combat support. Perhaps a skill that lets you use heavy machine guns, and these HMGs could actually sap some stamina from enemies they fire on (to represent suppression).
Or perhaps a mortar? The SOP system and a mortar would work great as your teammates could help you find targets to range in on. Mortars would help in longer fights based around objectives. And we've seen Snake using a mortar in a screenshot of MGS4. They'd be useful, but it leaves the mortar crew exposed to anyone who sneaks behind the likes to take them out. And if they're bad at what they do the SOP friendly fire lock takes care of that.
One thing MGO really needs work on is the cover system. Mainly it's useless. Especially for those who aren't used to the western styled run and gun twitch shooters. It's just too slow and cumbersome to use.