Here's some how/why, at least as regards frameworks designed for cross-platform development.

Cross-platform frameworks push developers towards lowest-common-denominator UI design -- you can only use the UI elements and interactions that are supported on all the platforms you target. So if there's a mediocre way to do something cross-platform and a more "Apple-Like" way to do it that isn't cross-platform (or which hasn't been baked into the framework yet, assuming it ever will be) a lot of apps are going to do it the mediocre way. (This doesn't really apply to games, as they usually have their own from-scratch UIs. But for every other kind of application it's absolutely going to be an issue.)

So say CS5 comes out and suddenly there are thousands of new developers who have never written for iPhone/etc. before, who only know about the features and interactions supported by Adobe's framework, and who, because they're Flash developers (sorry for the snark but I doubt it's far removed from how Apple sees it), wouldn't know what to do with a set of human interface guidelines to save their lives. I think it's safe to say that a large percentage of these developers will be delivering apps with interfaces that would be rejected if submitted as native apps -- but which developers using the native tools (and therefore steeped in the platform's ecosystem) would never have designed in the first place.

If Apple believes something's about to happen that will result in a significantly higher percentage of rejected applications, it's far easier for them to issue a blanket ban on it today and take all the heat for that decision in one blast than it is to let the can of worms be opened and deal with a new flood of problems on a case by case basis. I don't know if this is really their thinking but we'll find out, if the developer agreement is refined in a way that allows some of the dev processes discussed in other threads here as collateral damage.

There are other issues. Say CS5 had come out a year ago, and there were thousands of Apps in the App Store that used the Adobe framework. OS4 was released to developers last week, and all the native devs have started working with it. If OS4 breaks something for them, they're going to know about it and in all likelihood have a fix out by the time OS4 streets. But if OS4 breaks something in the CS5-built apps, the developers of those apps can't do anything about it until Adobe fixes the problem. You can argue that that's the developer's fault and the developer's problem, but when the people who bought those apps switch over to OS4, those users aren't going to think "god, how stupid of the developers to rely on a third-party framework by Adobe, a company whose reputation for timely bug fixes leaves much to be desired" -- they're going to think "Hey! OS4 broke my apps!". That's Apple's problem.

That's some of it, at any rate.

(Just to be clear: I'm not arguing that Apple only did this with pure, consumer-friendly motives -- I'm sure the Adobe/Google-kneecapping implications of this decision were very prominent in their minds if not the main driver. But there are also pragmatic benefits to Apple that have nothing to do with its effect on the competition.)