Getting back to the original question, Ross, another benefit of the Flex compiler - whether you're writing MXML or AS3 - over the Flash IDE is that all the source files for a Flex app (barring assets - images etc.) are text files. Text files are much easier to deal with in version control systems such as SVN or CVS - and version control systems are critical for development within a group of developers.
I may be totally martian here, but ... hmmm, besides the FLA part, you can externalize everything in text files too (no code in the FLA, just assets (and even...) and external AS files).
This is making me think that, as always, there are big differences between the framework provided and the technology used.
Start from nothing, use Flash, try to build up a framework (at least, some app building logic), all on your own, and/or with the help of other Flashcoders. Then, you discover Flex, and this gives you the framework (ie: geniuses thought about this for you). You stick to the framework, learn to structure code / applications, and then get on the next part: being efficient.
With both you can be efficient. As a proof, all the best Flash sites are Flash, not Flex. But all the best Flash apps are Flex, because it is ... just simply ... simpler.
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