I like your ideas about the animated flooding. The water and gas leaks in the SH3 Control Room were nice touches. Personally I'd like to have it so you can roam freely around the sub, like a first-person shooter and see the various compartments filling with water or on fire etc. Have a fully animated crew too, who run around bumping into each other and stuff. Think of the programming difficulties, of getting the collision detection right, having all this going on inside a pitching, rolling sub?
By the way, when you dove or surfaced in SH3, doesn't the interior tilt the wrong way? That always bothered me.