I gave up on the synced reading position at the same time I sold my Kindle, but I can live with that.
Getting stuff on the device is a bit of a hassle too, because I can't exactly go plug it in to my NAS, but exporting 50+ books to a directory and copying them manually takes a few minutes and I'm set for a year or more - so it's time well spent :D
Having everything (except for comics) consolidated in one place is the main reason I tolerate Calibre's quirks and eccentricities. It's ... opinionated, but it's still by far the best tool available for the price.