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I am a big fan of Flash Builder. You can build great desktop web applications as well desktop applications that run on AIR (installs locally to the desktop).
I found it easier to pick up Flex (now Flash Builder) primarily due to the resources (Learn Flex in a week video tutorials http://www.adobe.com/devnet/flex/videotraining.html ) as well as a big developer community that posts a lot of how to's and walk throughs. In my personal opinion, I think the power of Flash Builder/Flex framework is the ability to create what traditionally was seen as desktop apps within your web browser. If you're looking to create a basic crud interface, skipping Flash Builder and just doing it in PHP may be the way to go. If you're looking to add visualizations (ie graphs, charts) or highly interactive user interface to it then Flash Builder would be a good way to go (though keep in mind that you will still need PHP (or some other server side application layer like coldfusion) to interface with your mysql database but Flash Builder's dataservices creates some sample php classes for you to handle CRUD using Zend). There's lots of amazing things you can do with Flash Builder. I'd recommend checking out some of the samples from Tour de Flex to get a sense of what can be done with Flash Builder.
A couple of notes though - You can build and package native mobile apps with Flash Builder but if you're looking to create web apps for devices like iphone and ipads, Flash Builder isn't the solution since it compiles web based apps to Flash and we all know how idevices don't play nicely with Flash.
Thank you, very much, for your very thoughtful and well-articulated answer. It definitely addressed most of my concerns.
If I can ask you to elaborate just a little further: I think what is also "scaring me" from beginning with Flash Builder, aside from just tackling a new technology and knowing whether it is appropriate (items you addressed), is the fear that I should be working to learn some other emerging technology (like HTML5, PHP; Muse, Edge, PHP frameworks) when Flex and Flash Builder may be "on their way out."
I'm reading and trying to interpret the significance of the following article: http://www.rivellomultimediaconsulting.com/the-future-of-apache-flex/?doing_wp_cron=133640 6635
Now again, keeping in mind my "new-to-programming" status and my focus on creating a MySQL management tool, is this something that should steer me in a direction other than Flex and Flash Builder? Maybe HTML5, etc., isn't even that relevant to what I'm trying to achieve. My primary vocation is as the pastor of a church, but I also do work on the church website and database. I don't want to invest what little time for application development I have in the wrong direction.
Your help is, again, very appreciated.