AIAB is still awesome only "frozen in time", in fact Bloodwych acknowledges that his productions were inspired by it.
I use mainly AmigaOS 3.9 plain (no Amikit...) because I am more comfortable with GUIs, and I like my system files to be updated (Boing Bags..) and to have everything at hand.
WB 3.1 is more popular on EAB, and since the debate whether 3.9 is bloated / not really innovative or not is endless, I don't bring it to people's attention that I favor it. I think there is a lot to learn simply for installing OS 3.9 over 3.1 (I've read it's better to install it from the emergency floppy... Another debatable issue). If I had one remark : I'd like ClassicWB advanced users to have a dedicated forum, I am under the impression quite a few "tricks" need intensive EAB searches to be revealed.
If you don't run into problems anymore, you should worry, Amiga emulation is all about teh problems ! Just joking, as I posted earlier, you could run a few preinstalled games in a row, trying to spot a bug or room for improvement in one of the slave features.
Last, WinUAE is great but I think it's wise to know what you don't get with it VS the real thing. Fortunately, there are quite a few threads that deal with this.