I can't speak to all your concerns but I'll comment on what I can.
I own both a Kindle PW3 and a Kobo Glo HD (and others) and I use KOreader on both. I like KOreader - its 'night mode' is a killer feature for me as I generally find the lighting on ereaders skips from too dim to read comfortably, too feeling like it's too bright. But as you say it doesn't support any kind of note-taking which is a shame.
I use PDFs at work for technical manuals and view them on a PC and that's fine. I've never found the experience on any ereader that good. It's gotten better but I still avoid PDFs, which as I mostly read fiction I can do easily.
On Open Source etc. - Kobo is a little bit more open. Both companies provide closed-source reading/interface software. Kobo support epub as well as their own proprietary format (sometimes known as 'kepub'). They support Adobe-DRM'ed epubs so you have a number of different vendors you can buy from. Also that means it's easier to find library support. Amazon primarily support their own formats and they seem to be making them harder to reverse-engineer. (see the thread on 'KFX').
It's easier to install 3rd party software on Kobo. Going back a few years they actively encouraged it and indeed provided sample code etc. These days you get the feeling that they merely tolerate it, and the code is increasingly out of date. Amazon on the other hand clearly want to lock down their devices and you need to jailbreak a Kindle to install 3rd party software like KOreader. There's also evidence that they deliberately try to close off the loopholes that allow for jailbreaks, in successive versions of the firmware.
FWIW I think Richard Stallman's objection is to DRM and closed source (he would say 'non-free') software, so neither Amazon nor Kobo would cut it. You have to decide whether you're as much of a Free Software purist/extremist as that. I'm not.
I guess my experience overall is that I'm slightly more in the Kobo camp. Kindles are well-made and their software tends to be a little more stable. But Kobos are often nice too and they are more flexible, even with the standard software. For example Kobo supports the side-loading of fonts without the need for a jailbreak+'hack'.
Not sure if any of that helps. Feel like I may have rambled a bit. Oh well
