1. Return policy. Amazon has the best ebook return policy in the business. It seems essentially the same as their physical book policy. The last time I checked, Google Play was next-best (7 days no-questions-asked, regardless of jurisdiction) and everyone else grudgingly had a return policy where it was required by law (i.e. Europe) and none otherwise.
2. Sideloaded books. AFAIK, of the major ebook retailers, only Amazon and Google will let you sync books you didn't purchase from them to your cloud library. Other retailers might let you read sideloaded books in their clients, but you have to use Dropbox or an equivalent for backup and syncing across devices.
3. Client support. If it supports third-party applications, Amazon makes a Kindle client for almost anything you might want to read an ebook on, plus they have a web-based reader. Meanwhile, Google and Apple are busy paying "strategy taxes" for platforms it isn't in their interest to support, and B&N and Kobo don't quite have the resources to keep up.
In any case, since you can just open the files in the desktop version of Kindle, it doesn't seem like it would be such a big deal.
I have a Paperwhite and I couldn't be happier with it. It's the best manga reading device I own and it does a pretty good job with PDFs.
I've resorted to using a camping headlamp set on "red" (not as bright/obtrusive) when I want to use the kindle to read. However, I mostly just use my phone and the Kindle app.
Advances in the display beyond the gen 3 (first I bought) didn't merit any sort of upgrade for me.
Mostly a tongue-in-cheek comment but somewhere deep in the halls of Amazon I bet that discussion was had...
They're very profitable, but reinvest almost all of their money.
http://ben-evans.com/benedictevans/2014/9/4/why-amazon-has-n...
(And apologies to my friends who work at Amazon, but let's be honest: you're all going to quit within a year or two to work somewhere that's less abusive of its employees.)