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The simplest answer to your question is if you are doing a lot of linear animations/presentations and "traditional" flash asset creation then you will want to stick with Flash CS3. However, if you are building robust applications that require dynamic data presentation and/or user interaction then you may want to take a stronger look at Flex.
Feel free to ask anymore in depth questions...
You can find out about academic pricing for Flex Builder 2 (the current release) here: http://www.adobe.com/education/purchasing/education_pricing.html Academic pricing for Flex Builder 3 has not been announced yet.
Also, bear in mind that Flex and CS 3 work great when paired together. You can use Flash, Photoshop, etc. to craft the look and feel (skin) of your application, and then use Flex Builder to create the UI layout and code the business logic.
There was a few news stories today ( Oct 24th ) about Adobe announcing Free Flex Builder 2 for Education ..