It's really not that complicated. You download them from a web interface and you drag and drop them into Calibre (with a de-DRM plugin installed). Done, they're now available together with all the ebooks that you got from other sources.
Having all the purchased ebooks in one place is more convenient for me, not less. The alternative isn't a different book store, it's pirating. While I do have an appreciation for all the books I got from DRM-free places, I don't pick what I'm going to read next based on where it's available. The majority of the books I want to read are available on Amazon, and breaking their DRM is very easy. They wouldn't get my money if any of those two were untrue. I'd probably revert back to pirating.