The obvious reason being that Flash is the overarching platform with many tools, IDEs, runtimes, et cetera and Flex is a framework used to produce Flash content. Flex Builder has always produced Flash (NOT FLEX) and I’ve encountered many people who just never could grasp this fact. This will help clarify things for so many people. Unfortunately, there will probably be a pretty big backlash from some sides as well.
Ted Patrick (@adobeted) announced the change over Twitter this evening. There’s a lively conversation going on now: Join in!
UPDATE:
Read an official statement from Lee Brimelow or Serge Jespers regarding the change.
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