I buy Android devices for stock Android, not for a manufacturer skin.
You're very much in the minority. People like iOS because it's integrated and easy, that's the same thing Amazon and Google are going for as well.
"What comes on Nexus devices" is what I consider a stock Android product. That's effectively the selling point and why it's so fantastic.
The integration into Amazon's ecosystem is a major selling feature, trying to fully tie it into two ecosystems would be a mess.
You can use other video services though, Netflix works great. For music there is Pandora and Spotify.
You can certainly use other services like Netflix, Hulu, Spotify or Pandora. Amazon probably loves that those apps are available for their device. The basic reason is that once you go looking for something not available on those other services (which happens frequently) your only other real choice is buying it from Amazon.
I have a fire, and it was immediately obvious within a few minutes it's designed around consuming content from Amazon and spending more money with them. While it would be absolutely a mess to fully support two app ecosystems I think it's naive to think that Amazon would have supported any system that didn't primarily direct funds back to them. They can sell these devices so cheaply as it doesn't matter if they profit from hardware. They've designed everything in such a way as to derive their revenue from sales of media.
It's a selling point because it's easy and it's automatic. Similar to iOS. Out of the box you're ready to go and if you buy something one place it shows up in the other place too. If you're a Prime customer there is a ton of video content waiting for you for free. It's a walled garden, but other than Apple it's the most well done walled garden.
I'd prefer top of the line hardware with stock Android (mostly so I can test stuff), but that's not the business they're in. They made that very clear with Bezos stating they don't want to make money with selling their devices, they want to make money when you use them.
That said, I'm seriously curious if Amazon is still using a highly modified, improved, Android 2.x fork for their release version.
http://www.ubergizmo.com/2011/11/kindle-fire-sideload/