Yeah it has these things, but the game isn't balanced around them from what I understand ala Twin Snakes ...so yeah, kinda superfluous and what you get in return is a horrid framerate/PQ
I thought they were pretty well balanced.
Unlike Twin Snakes, which added gameplay elements that the game wasn't designed for, the MGS3D additions simply expand on Snake's existing abilities.
-Crouch walking doesn't really decrease your camo index noticeably, but allows you to position yourself quicker behind waist-high cover then crawling or wall-hugging (most useful in firefights, to be honest).
-Third-person aiming helped if the low resolution prevented you from aiming weapons in first-person well.
-When you're moving while aiming, you move slower then when you're running, so you're still vulnerable. It's more of a positioning thing.
-Being able to crouch while holding a guard opens up more areas that you can use to safely interrogate/dispatch guards at the expense of movement.
Overall, they just make Snake more mobile and less awkward to play as. They each have drawbacks that need to be considered, and I think it could actually be argued that some of the changes aren't effective enough (if crouch-walking lowered your camo index a bit more, it'd be much more useful).
Personally, I think it's a shame that the 3DS portmake is the only version of MGS3 that gets those expanded abilities, but at least there's MGS Vita to look forward to (if KojiPro wasn't kidding about releasing a Vita version of all their future titles to support transfarring).