I jailbroke my Kindle and moved to KOReader last year, primarily to get away from the Amazon jail. Just the bare KOReader UX was pretty utilitarian. It lacked polish for sure. I'll have to agree that, as noted elsewhere, the KOReader menus can be difficult to get a grip on.

If you're working at just the most basic level of functionality, I don't think KOReader is necessarily worse than native Kindle. The latter is hampered by being very opinionated about how you should experience it, and that includes pushing their store above the user's own library, and this is a real annoyance.

As you start to demand more capabilities they diverge more. Organizing when you've got many books on the device is clunky on both platforms, but in different ways. The native Kindle options for grouping are simple, but not necessarily easy. They're very generic, and very cumbersome to work with. Bare KOReader's support for folders makes more sense to me, and it's easier to deal with bulk books than is Kindle's.

Getting books onto Kindle is super-easy if you get them from Amazon, but complexity ramps up for other sources. Your best bet is plugging it into USB and transferring via the file system. Native KOReader add to this an OPDS capability (if your book repository supports it), which works but is less than pleasant. If you use BookOrbit as your repository, there's a plugin that gives you the remote BookOrbit UI from the Kindle, which makes things a LOT better.

I experimented with Simply UI for a bit but could never get it to work quite right. About a month ago I found Bookshelf, and this makes the UX pretty wonderful. It has a very attractive and intuitive UI. And it simplifies the interactions needed for group management a bit.

Bottom line is that KOReader + Bookshelf are, for at least a power user, a potentially far superior experience compared to baseline Kindle.