Sony fixed the screen with the PRS x50 line. The T1 and the Kobo touch have identical Pearl Eink screens. If you thought your Cool-ER screen was good, just wait until you see the Pearl screen.
The Sony will export notes; how much text comes with them depends on publisher permissions with the DRM encrypted books.
The Kobo and Sony both use normal styli. Anything that can write on the screen without scratching it will work. With the T1, the stylus no longer fits into the reader when not in use.
Battery life should be about the same for both, depending on whether you have WiFi on or not.
Sony has the best reputation for handling PDFs, but PDF is a horrible format for a book. None of the readers will deal well with PDFs that are images or that have lots of charts, tables, or figures in them.
It's my opinion that Sony does the best job of helping me manage my books on the device. The Kobo seems much more basic and was released with a lot of bugs.
You can adjust how Calibre sends books to your Cool-ER. It doesn't have to be author folders.
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