The great thing about the Arduino environment compared to every other "educational" system I have investigated is that you're not trapped in the walled garden. If you want to toggle a pin with a direct bitwise write to the port then you can do that without knocking down the other nice parts of the environment like the convenient millis() timer.
So if you're an experienced AVR programmer, you should fit right in once you discover the parts of Arduino that are actually useful to you. You don't have your hands tied. The hard part is learning to reach out and find what parts are useful. I've seen a few while(1) loops created by experienced programmers that are counter-productive to the Arduino way of doing things.