Workbench 3.x will run on any Amiga.
(Even a modified A1000)
3.0 and 3.1 will run fine on a 2000..
I haven't used 3.5/3.9, and they should run, but I'm not sure if they might be sluggish or not (wanting more CPU/RAM depending on your 2000 setup). I've heard people say both...
But there's no AGA requirement for 3.x.
desiv
p.s. This implies you have upgraded upgraded your Kickstart ROM also..