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Operating system and ecosystem
Two totally different platforms.
- The iPad Air runs Apple's latest iOS 7 operating system, and apps are restricted to those available from the App Store.
- The Kindle Fire HDX runs a heavily modified version of Android 4.2.2, which Amazon calls Fire OS 3.0. Apps are restricted to Amazon's App Store and users cannot use Google's Play store.
See also: The very best tablets of 2013
To be honest, when it comes down to which app store is best, it is pretty much a matter of personal preference. Apple's App Store is probably the biggest and best curated, but there's nothing wrong with Amazon's offering either. I use both, and while on the whole I fnd that Apple has a better selection of apps, Amazon's it not bad either.
If you're already locked to one ecosystem or another then this might sway you, but otherwise it's not really much of an issue which you happen to choose.
(Image source: Apple and Amazon)