I was pondering the purchase of 3.5. How well will it work on a 68060/50-based A2000?
It should work great. It ran very well on my A4000/060 @ 50mhz. Especially with a RTG graphics card.

I heard 3.5 is 3.1 with some user-added extensions. Can someone confirm? 
Pretty much. Honestly, I'd say AmigaOS 3.1 was the last real update. 3.5 and 3.9 are really pretty minor point updates. But they build-in some features and patches that are rather annoying when not included.
My own advice to you might be to go for AmigaOS 3.9, as it includes the full version of the Genesis TCP/IP stack, rather than the unregistered Miami included on OS 3.5. Very handy if you want to get your Amiga networked.
