If you have a large collection that you actually plan on reading, I don't think I would recommend a Kindle.
You can't really organize things very well, you only have collections that are just one folder deep.
So if you have a lot of books, you either end up with a lot of collections, or a lot of stuff in collections. Either way it's a pain to navigate as there is no way to quickly scroll through each page of items. I just hit 200 books on my K3 and it's gotten to be rather unwieldy. I can't imagine someone having 1000s.
I have no idea how other e-readers handle organizing books, but the Kindle is very barebones.