Normally I would do propaganda for Pocketbook at this point, but for me the shape of hardware (i.e. your last point - general comfort) is vital, and Pocketbook 3 is vastly overshadowed here by Pocketbook 2. Pocketbook 2 has wider bezels so you can hold it in comfortably in any orientation. Page turn keys are wide, comfortable, and work regardless of the angle of pressure. Pocketbook 3 is much worse to hold and handle compared to Pocketbook 2.
Then again, Pocketbook 3 has 1GB of RAM and a crisp 300 ppi Carta screen over Inkpad 2's half GB and dated Pearl screen.
Kobo Aura One has as thin bezels as Pocketbook 3 (too thin for me). Kindle Oasis (even the 7" version) is simply too small to be a serious research tool.
For PDF viewing, any Pocketbook in my opinion surpasses, due to cropping and orientation options and pinch zoom, all Kindles and Kobos. On the downside, highlighting is not comfortable to do on Pocketbooks.
To make PDF files tolerable on a Kobo, there's the Koreader app
https://www.youtube.com/watch?v=i2oSOeAnD10
If highlighting and annotation will be your main preoccupation, I recommend investing a bit more and get an Onyx Boox Note: 10" screen with Android 6, i.e. practically limitless choice of additional apps, including for bookshopping on the device. Onyx Boox Note, as the name implies, is specifically geared towards notetaking.