Having owned, played and completed both on my iPhone, let me say this-
If you want a fast paced, lots of shooting, running around type game, go with N.O.VA. Enemies are more common, less difficult (quantity not quality type scenario) and you'll find yourself in more of a Halo type gameplay setting.
With MCS, the gameplay is a bit more paced, enemies are a little more taxing, and there are more cutscenes which IMO slow down the shoot em' up feel a little. This game is good though for sniper action, precise grenade hits, peering around corners, etc. It does have some fast action levels but for the most part is a little slower.
In terms of graphics, they are pretty similar, with N.O.V.A having maybe a slight edge. I enjoy the N.O.V.A online play better, as it's a bit faster and more intense. Based on all that, you'll have to make the best informed decision, I'm sure you'll be happy with either.
Bang for your buck: Depends
Good controls: N.O.V.A
Replay value: N.O.V.A