OS2.x uses a black menu bar at the top of the Workbench and other system friendly screens or programs, but Workbench 3.x uses a white menu.
If you want to make 3.1 look like 2.x (the original 3000 OS) then you can easily turn the menu to black by using VisualPrefs (
http://aminet.net/package/util/wb/VisualPrefs).
There are some other minor differences in the window gadgets as well, but nothing major. If I was you, I'd make two bootable partitions. The first one OS3.9 with all the trimmings, and the 2nd one OS2.1 (last and best 2.x release) for when you want that original A3000 look and feel. You would need Kickstart 2 though to get the black menu bar and old style gadgets.
Edit: PFS3 supports OS2.x, so you can also have large drive support if needed on your 2.1 installation.