Amanita Design, creators of the indy award winning flash-based game "Machinarium", recently released this title to iPad. Machinarium is a basic point and click puzzle adventure. If written in native code this would have no issue running on even the first iPhone (of which there are plenty of similarly detailed games.)
However due to using the Adobe iOS tools(air etc.) The performance is dismal on iPad 2. iPad 1 owners have mostly sought refunds, and left bad reviews - forcing the developer to make the game "iPad 2 only" despite being a battery killing lap heater. (This already puts it in the apple cross-hairs as it's available to download to iPad 1 users.)
Discontinuing flash player is only half of Adobe's problem, the bad code is still being manufactured into processor-heavy apps which sap battery life and demand far-higher specs than what would normally be required if writing in native code, as noted in the example above.
The crux of the problem is that it's not a small amount of additional processing overhead, these basic apps are churning through battery via excessive cpu time.
These tools from Adobe are allow developers to port their flash games to the app store, and instead of increasing their revenue, it's creating problems and damaging their image/fan base.