I have worked with Flex Builder 3 using PHP as middle layer to back-end. I was able to test/debug seamlessly, stepping thru the flex code and the php code, via Zend Studio. Would I be able to do the same with some other IDE for Java, like Netbeans or Intellij?
I recommend intelliJ for Flex development especially when doing Flex with Java or Grails or for any jvm language for that matter. intelliJ currently has support for Grails that no other really has at this point.