I actually downgraded from OS 3.9 to OS 3.1
This was my setup on my a4000 and a3000T and
this is my current setup on my a2000 and a1200. Although my a1200 and a2000 could easily run OS 3.9 I prefer OS 3.1, it's smaller and faster.
I've got a nice OS 3.1 setup with different options at boottime:
No action > Scalos 1.2d
Left mouse > Opus Magellan II
Left mouse and Shift > plain Workbench 3.1
Right mouse > CLI with Parm