Reading PDFs on Kindle Paperwhite is much more comfortable with KOReader. Thanks to https://www.willus.com/k2pdfopt/ it can crop pages and reflow text unlike the native reader. It's not the best experience with some types of documents, but generally it works very well.

I don't have a solution for synchronization at this point. My current workflow is quite involved: import a document into Calibre, upload it to Kindle via Calibre wireless connection (KOReader supports it), read and highlight, get the modified doc back to Calibre, extract highlights with https://github.com/0xabu/pdfannots. It'd be more convenient to send new highlights from Kindle somewhere immediately without transferring the document itself. I haven't looked into it, but I believe it should be possible with a KOReader plugin.