I've replaced the SD card in mine to a faster variant and that seemed to have helped with speeding things up a bit. On the stock reader, KEPUB is the way to go as EPUBs are really slow due to a different
renderer being used.
I've also noticed that certain fonts or books (I assume there's some weird CSS or HTML in them?) seem to bog down the reader. Once I get rid of the offending party, it's back to its usual self.
I also do occasionally vacuum KoboReader.sqlite and convert book covers to grayscale with Covergen, but perhaps the impact of that on device speed is a placebo?
