Apple doesn’t want apps that don’t feel like native iPhone apps on the iPhone. It doesn’t want Adobe to aid developers in creating a world where App X for iPhone and App X for Android are indistinguishable from one another. Apple doesn’t want to introduce new iPhone features and then watch as nobody takes advantage of them because Adobe hasn’t updated its development system yet. Or, worse, watches as Adobe refuses to adopt them because the other operating systems don’t support those features.
Excellent write-up by Jason Snell at Macworld. It doesn’t just cover the Adobe/Apple situation, but other aspects of the iPhone OS 4.0 announcement as well.