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I've been fighting with the same thing. I have a app that I'm building right now, it runs quick in Flash but when I port it over to Flex it seems to run slow. It is pure actionscript 3 so I'm kind of confused on what is hindering the performance in Flex.
The best reason to choose one tool over the other is that you have something working in that language already, and are just extending it into the AIR world.
If you're starting a new project, you then have to balance tools you have and know how to use against the strengths of the tools. A tool you don't know has to have some pretty compelling strengths to make you take the time to learn it, unless you're just doing it for fun. If not for fun, the effort has to pay off, yes?
Very generally speaking, here are the strengths of the tools, as I see it.
Flash's main advantage over the others is in applications with lots of graphics and animation. The reason for this is purely because that's what the Flash authoring environment is geared to produce. It's not got a very good ActionScript editor, and as a consequence there's a practical limit on how much code you want to write in a given project. It's not a question of whether you can write a 20,000 line ActionScript program within the Flash environment, it's a question of whether it's better done in another tool.
You can combine them, of course. You could build a whizzy GUI control in Flash to use in a Flex application which is hosted inside a web page, for instance.
JKHGDKHGSLKJ is right on the money_
One additional mention about Flash is that it is never necessary to load an entire Flash Project into a Single Flash Movie_
The more complex Flash Projects are developed in a modular fashion so they become easier to edit one section without having to re-export the entire project_
Build small modules and load the SWFs into a larger Project SWF Template so even if your code does get up to 20,000 lines - it will break down to 10-100 lines here and there that are easily swapped out when needed_
Also if you know any server-side coding -- PHP -- ASP -- etc... Then this can also be tied in so to load content dynamically_ Thus the robustness of Flash itself_
Misplaced post. Please ignore.