Kickstart 3.1 was a bug-fix release. Many of the bugs are quite subtle but you'll need 3.1 if you plan on upgrading to 3.5 or 3.9 .
The most obvious bug is that the AGA fetch rates in the custom chips don't take advantage of fast-page mode rates unless you're in super-high-resolution mode. Kickstart 3.1 kicks it up to full-speed whenever it is possible to do so (and frees up a lot of bandwidth bottlenecks in the process.
