You can really boil the Fire phone's problem down to one thing: it's designed to help Amazon, not users.
The home screen fills up valuable real estate with a section dedicated to purchase suggestions. Firefly is primarily there to help you find things you can buy on Amazon. Third-party apps? Features that would be useful on a day to day basis? They get shoved to the back. The Kindle Fire tablets sold well partly because of really good pricing, but the Fire phone didn't (and arguably still doesn't) even have that advantage.
Contrast that with Apple. It may have a walled garden where iTunes gets special treatment, but the interface is still pretty neutral. You can shove all the official apps out of the way if you prefer to browse in Chrome, check messages in Mailbox and play music through Spotify. When new features come in, they're rarely there solely to simplify spending cash with Apple.