Lets see: I installed both OS3.5 and 3.9 recently on my A4000 and OS 3.5 rocks and does some major enhancements over OS 3.1 but OS 3.9 drags and Picasso 96 doesn't work with my rtg card--Merlin--in OS 3.9 and the drawbacks of OS 3.9 exceed the benefits and so now I have a triple boot system with 2 partitions of 3.1 with different video drivers for my Merlin card and a 3.5 partition with Picasso drivers.
OS 3.9 works great on my laptop with WinUae but I don't really need it with my real Amigas and the default system is still 3.1 on them. OS 3.9 is nice in a lot of ways but it consumes a lot more of the precious resources of classic Amigas and the video, processor, and memory upgrades for these systems are getting more expensive all the time. Think about what you use your Amiga for. I mostly run graphics applications on mine and don't really need 3.9. 3.1 covers the bases well enough and all 3.9 offers me is a lot of conveniences and eye candy. If, on the other hand, you are trying to surf the net with your Amiga, OS 3.9 might be worth your while.