The main advantage of the Arduino IDE (IMO) is that you can install it, load a program, and compile to board very quickly. Like, "following an amateur blog tutorial" quickly. And you have a good shot of getting it to work right away. That is where the advantage ends, though.
Yes, you can use better IDEs -- Atmel Studio for instance -- by copying all the Arduino libraries into your IDE's include directory and/or your project directory, and configuring accordingly. Then you're writing real C++ in a real IDE with a real compiler (the same compiler actually, but not hidden anymore.)
This is what the ARM world seems to be lacking sorely -- that instant gratification, trivial first experience.