There are some tangible benefits to 3.9 over 3.0. Aside from various bug fixes, it has a slightly improved Workbench, with ARexx port (which I found very handy), asynchronous file rename/copy/delete (never did understand why that wasn't always the case), tarted up icons, better scrolling of windows and so on. You get VinceEd as an alternative shell, which is rather better than the standard shell (though I always had a soft spot for KingCON). It also comes with a TCP/IP stack out of the box (though AmiTCP 4 is better IMO) and you also get support for larger disks, which is handy these days, since finding < 4GB drives outside of a computing museum is somewhat tricky.
You'll have to add the cost of kickstart 3.1 to that though.