I have found that the PPS 040 board for the Amiga 2000 works great with Kickstart 2.04 and Workbench 2.1. I can not get this board to work properly with Amiga OS 3.x. Most likely there are other Amiga hardware that acts the same way, works great on Amiga OS 2.x but not 3.x.
Odd, I have one of these boards in my A2000, running 3.1 with no problems at all.
I see no reason in this world to run 2.x these days. I tend to agree with the 1.3 to 3.1 jump (I am about to add 3.5 to the A2000 though - see how that works out)