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.