I think the underlying (and completely unsolvable) problem boils down to user experience. There are myriad flash apps out there with atrocious hover-state-based interfaces that are annoying on PC, and would be completely unusable on a touch screen device. Activating flash on a mobile device would open the floodgates to countless apps that simply wouldn't work, without providing context to the user as to why they don't work. In such a situation, it is simpler to control the user experience by simply not allowing flash.
Aren't there countless websites out there with no Flash and only HTML/Javascript/CSS that have atrocious hover-state-based interfaces that are completely unusable on a touch screen device?
Why deal with hover-state-based interfaces differently for Flash and non-Flash websites?
Is it easier to show a user a mobile version of the site (with no hover-state dependencies) if that site is non-Flash than if it has any Flash on it?
