Apple has put itself in a spot for more negative comparisons. If Flash runs better on Android, Apple looks bad. Even if Android devices have terrible battery life and tons of other issues, the talking point turns against Apple. It's a lone battle for Apple.
Suddenly Flash support becomes more important than battery life. But Apple knows that the average customer wants mobility with a mobile device. It cannot let Flash dominate the product perception.
My prediction: Apple will make a deal with Adobe and end the compatibility war somewhere in early 2012. They'll end up agreeing on a 2-way support deal regarding regular OSX and iOS-specific updates. Please let me know how you feel about this in the comments below.