Apple's fixed the criticisms from a few months ago (long submission updates, poor/inconsistent private API policy, etc). Not to say that you wouldn't have to look far to find new criticisms (their recent removal of "adult" apps, to name one).
Adobe, on the other hand, hasn't fixed any of their problems. And they've had much longer to fix their problems than Apple has. Hell, it took less time for Apple to create a problem that had to be fixed then for Adobe to fix their problems.
Well the Apple App Store problems were merely procedural issues whereas the Adobe issues are technically difficult problems that haven't been solved well by anyone and aren't helped by platform/codec war politics.
From what I know of the issue, the technical problems with Flash are not difficult to solve. The fundamental problem seems to be that Adobe is not willing to put in the effort to make Flash work well on multiple platforms.
Adobe, on the other hand, hasn't fixed any of their problems. And they've had much longer to fix their problems than Apple has. Hell, it took less time for Apple to create a problem that had to be fixed then for Adobe to fix their problems.