I think the 3.1/3.9 thing is really a matter of preference on an accelerated amiga... I keep a partition of each, but generally use 3.9 and revert to 3.1 for testing purposes. Either one will need a lot of tweaking for optimal use and performance, but 3.9 has a few basic features "built-in" which makes it less hassle overall IMHO. I haven't found any real compatibility issues with games or demos, and that's about all I use the amigas for.
Regarding speed, I didn't feel much difference in AGA WB operation between an '030 and '060, especially if you keep the screenmode reasonable. On the A1200, my 3.9 install takes maybe 1 second longer to boot than bare 3.1. :-)