That's it really, it comes down to what you want to do with it. Personally using a couple of Amigas, I have OS3.9 on my main one which I use for most things, and wouldn't have it any other way, but I also have a small one which I'm using as a retro games system, and that's staying on 3.1... I've used 3.9 on an 030 and haven't noticed any real difference speed-wise apart from the reboot at cold boot time. I know most of the stuff that's different you can get patches to do instead, but it's nice to have them there as part of the system.
