Here's one that should be in the firmware. The issue is the huge amount of wasted white space at the bottom of many pages, which is caused by stupid defaults for widow and orphan prevention.
Apparently (according to davidfor) the defaults for widow and orphan prevention are 3 and 3 (lines, I presume), which keeps the Kobo from breaking paragraphs across pages, but wastes a huge amount of display space and causes a lot of unnecessary page-turns. These default values may be appropriate for a magazine of a book, but are simply not appropriate on an e-reader, where screen space needs to be conserved, not wasted
If the defaults for both of these values were 0, perceived performance would be much better, and the annoyance factor would be greatly reduced.
Changing both values to 0 seems to work well on epubs - for the first time, text uses all the normally-wasted white space at the bottom of the screen, and goes all the way down to the menu-bar. You get several more lines/page on the average, and fewer page turns.
BIG thanks to textchimp for this one!