Cross compilation to native code from flash runtime was absolutely possible, and absolutely never considered by Apple ;)
Then a day or so before that feature left beta, apple added a vague new clause to their app store agreement, which made no sense on paper but whose obvious purpose was to disallow flash apps. They then unpublished all the existing flash apps for violating that clause. Adobe quietly cancelled the app publish feature, and a few months later apple quietly removed the clause.
Adobe AIR is actually still available today (now maintained by Harman through an agreement with Adobe), and it can still compile native iOS apps that can be submitted to the App Store. This feature was never removed, and is still maintained to be compatible with new iPhones.
There was briefly a kerfuffle about it, as people using other cross-compilation tools (xamarin? etc) worried their apps would get removed as well. But IIRC apple never actually enforced the clause, other than to remove existing flash-based apps and reject new ones.
No keyboard: which broke most games.
No mouse: touch is not the same and hard to fake mouse controls with touch while supporting pan or zoom.
Small screen: flash was designed for bigger screens and everything was too small or needed zoom.
Flash wanted to control its event/animation loop: battery life was drained quickly even for basic content.
Mobile didn't kill Flash.
You see the same UI issues when controlling a Remote Desktop from a phone screen. Just difficult.
Many Flash haters have no clue that before Unity and friends many of the first generation games on iOS were actually AOT compiled Flash games, despite Apple.