I wouldn't be too concerned about SE abusing 3D

Though the more I thought about it, the more I thought it would be a good way to simulate the Mode 7 effects during airship travel.

I'm just impressed the 3DS is powerful enough to play MGS3, a game most people still can't believe the PS2 can actually play. That's some seriously powerful handheld hardware we're talking about. I just hope they keep the Opera scene interactive and not relegate it to a complete custscene if they go that route.