Here is an interesting idea.
Perhaps you could crack the format of the Kindle .mbp1/.azw3r/.azw3f files, extract an up-to-date listing of kindle annotations, and convert it to-from a plaintext representation to keep in a custom column. That would allow syncing annotations between Kindle devices at least, without resorting to My Clippings.txt -- which is nice in terms of listing annotations, but would be even nicer if it was incorporated into the book itself.
I think the annotations plugin would really benefit from some serious work done in that area, but no one seems to be interested. (Including me sadly
though I would be grateful for anyone else's efforts.)