I will second reading PDFs on your tablet, it's not pleasant to read them on
any e-ink device.
The Kindle will save annotations when created on the device, (but not if the annotations were merely synced) to a text file in the documents folder, called "My Clippings.txt". The Annotations plugin for calibre can save these to a custom column.
http://www.clippingsconverter.com/ can aggregate your annotations from "My Clippings.txt" and convert them to a .xlsx
I do not know what options are available for other devices, but the Annotations plugin only works with Kindles, and the Marvin and GoodReader iOS apps.