Another thing is you want to make sure you got a fast Amiga, such as a 030 50Mhz or above if you want to be happy. Otherwise life with Amiga OS will slow down a bit.
I've been VERY impressed by OS 3.9 myself, I really can not see any reason not to update unless you are waiting for OS 4, or simply have an unexpanded Amiga.
Life with OS 3.1 kinda sucked in that I had more Guru errors and I had to download and istall a TON of extra crap to get it to work half as well as OS 3.9. So basically I'm saying 3.9 is a GIANT leap!
Works with Dopus Megellan too!