I thought of another thing: Way back in firmware 2.8.1 the font hinting might not have been enabled by default, which in later firmware it is. In current firmware the built-in stylesheet has an item
body { -kobo-font-hintstyle: 1; } to turn on hinting which doesn't seem to be present in firmware 2.8.1
There have been a number of observations that hinting doesn't seem to help on an e-ink screen, and there are some cases where it makes the font look much worse. You could try turning off the hinting in later firmware and see if that makes it look more like what you see in 2.8.1, either by modifying the kepub book's stylesheet to set
body { -kobo-font-hinstyle: 0 !important; } (I haven't tested that) or by stripping the hinting from the font itself.
Edit:
This post has screenshots showing a (fairly extreme) example of how much a font can be improved by removing the hinting.
Edit2: Firmware version 3.1.0 was the first that had -kobo-font-hintstyle: 1; in the stylesheet.