MGS on the 3DS looks sweet, although I have issues seeing the enemies on it. The 3D aspect of it though is very nice, I thought.
Castlevania doesn't have to be in 3D to be on the 3DS and still make use of the hardware. Now, I agree the Vita would do a 2D or 2.5D Castlevania great justice because of the better colors. But at the same time, the 2.5D aspect, or even 3D aspect if they went that route, wouldn't be as impressive. Sure, the colors are nicer, but you lose the true sense of depth. Shinobi and the cutscenes from Ghost Recon on the 3DS (I wish Shinobi used 3D on their cutscenes and not just in-game) are 2D but look good in 3D, because in 2D mode it looks like it's all drawn on one plane, but when you switch to 3D mode you find out it's drawn across multiple planes. It's very well done on Ghost Recon.
And another thing I noticed yesterday in Ghost Recon - if you play in 2D mode, you can't see the clouds passing over the field. When you switch on 3D mode, moving clouds appear.