I love my Kobos. I've effectively sold quite a few based on how well they work (most of my social circle reads on Kobo now).
In addition to "Ok, fine, you can do that thing you're doing anyway" with the recent updates, the SQlite approach works fine and has remained so for... oh, years, at least.
The stock PDF reader is fine for ebooks, but sucks for reference PDFs. However, it's trivial to install koreader, and that is good for reference PDFs. I replaced an iPad and GoodReader with a Kobo Elipsa and koreader for reference docs, and it's great. Plus, insane battery life with the backlight off.
And if you want to install some goofball bit of software, well, drop it in the right directory and don't go whining to Kobo if you break things. it's an insanely hacker-friendly device that's also a solid e-reader.
I've been following the Pine Note work with some interest, but, really, all I'd want to do with it is stuff koreader on it and use it like a Kobo.