A lot of my wish list has been addressed by others, so here's some more:
Support for more formats. I have Kobo's reader, Overdrive's reader (handle's Adobe's DRM), Adobe Reader, Amazon's reader, and a DjVu reader installed on my Vox. There are a few other common formats out there too, and they require separae apps. Kobo could integrate all of that (except for encrypted MOBI) into their reader and make everyone a lot happier. After all, it would make it easier to find stuff in library (everything is in one place) and reading life would be more meaningful (I like the basic stats).
Ensure that the reading experience is on par with the Touch. There are a lot of small things to deal with here. The dictionary, highlights, and notes are poorly integrated. Kobo uses it's own menu for some things, and Android's menu for other things. I have to tell it to update the library manually. We need a true factory reset (this is arguably more important on the Vox since more people are hacking it).
As for the hardware stuff, I definitely agree that the next version needs a sliding or recessed power switch, a longer cable on the charger, and a better speaker. And please work on the weight! I have no idea why, but it feels like it weights 10 times more than the Touch even though it's only twice the weight. So trimming a few grams will probably make it much more pleasurable to read on.