Since this is a thread about danmaku engines I guess I could post my input as well.
I'm creating a bullet hell game for TIGSource's Assemblee Part 2 called Lowblow - Fantastic Awakened Passion:
<img src="http://i48.tinypic.com/903ybl.png">
<img src="http://i46.tinypic.com/2uprbq0.png">
I decided to simply cheat when it comes to the 3D backgrounds, which works quite well - the current test level thing looks reasonably convincing enough. It's also built with variable level progress speed in mind, and doing stuff like adding different objects to the background scenery shouldn't be hard. So really, 3D backgrounds aren't a showstopper for making your danmaku engine, you just need to cheat a little