3D graphics on the Amiga chipset is a whole other business than in VGA. I think a lot of the rendering code in Wolfenstein 3D is built around the idea that the computer is using a linear frame buffer. If you take that away, there's a lot you have to change in the code (more so than in doom or quake) to make it run acceptably in planar ECS or AGA modes, and still, you'll never achieve the same performance without a much faster processor.
As for the FPS games that actually run acceptably on a stock 1200 (alien breed 3d, gloom, ..?), they similarly use platform specific tricks to pull it off.
I think A1200 should be quite capable, specially if you use 16 colours like unofficial Atari version done by Ray and a atari-style c2p:
http://www.pouet.net/prod.php?which=17247&howmanycomments=25&page=2http://www.pouet.net/topic.php?which=3838&page=2
