Normally 3.5/3.9 would run slowly on a 030/25 if you were running in ECS, but since you have an RTG card its possible that the component that normally slows these systems down won't be as slow on your system, picture.datatype. It won't need to remap and dither every single image it loads down to 16 colours, it should be able to spit them out instantly in 24bit, speeding up booting and loading times, especially for image-laden applications like YAM.
Many of the patches people normally apply to 3.1 or AGA systems won't be needed. FBlit, FText, BlazeWCP are all unnecessary if you have a graphics card. The only patches I'd recommend are VisualPrefs and Birdie which will help spruce up your Workbench.
I don't think you should just rely on the opinions of a bunch of random people on the internet though, just install OS3.1 and OS3.9 on separate partitions and try them both yourself.
