3.9 Is great, but is a bit 'bloaty' by AmigaOS standards - It needs a good accelerator + decent amount of RAM to work well. I'd say it's best suited to virtual systems like Amithlon, X-Amiga, (Win)UAE...
3.5 Is probably better for a 'real' Amiga - Most of 3.9's features with a smaller 'footprint'.
3.1 Unless you're an eye-candy junky (like me) it's hard to justify the move.
? Hear me out... My A1200/060 with KS 3.1 & WB 2.1 runs like nothing you've seen! No, it's not pretty, but it is fast + functional when in that mode.