Bear in mind that from my perspective I'd already be downgrading from Xmega to Mega and downgrading the IDE as well would make Arduino a retrograde step for me. Perhaps I'm barking up the wrong tree with Arduino, but I'm hoping not.
I'm kind of with Robin2 on this, not out of being a arduino evangelist, but more from just simple practicability and experience. Have you actually used the arduino IDE and identified whatever 'retrograde steps' you think you are forced to take? If so please list them and we can comment on if there is a work around or misinformation on your part. If you don't have any experience using the Arduino IDE then I suggest you use it for awhile and take notes as to issues or features you can't live without and maybe someone here can help you with them. There are many, even professional software types around here (not me, my favorite programming language is solder) that seem to have no problem using the arduino IDE with whatever limitations or tools they don't get to use like at their work place.
The arduino IDE is simple on it's surface (and that was on purpose) so it certainly doesn't pretend to be a full on professional programmer's IDE, but it does have features and preferences you may not be aware of. For instance many experienced programmers complain about the rather simple text editor the Arduino IDE uses, but are you aware that one can set up a preference to have the IDE utilize any text editor you wish to use?
Keep in mind that the main objective of owning an arduino board is to build something interesting or fun, it's by no means meant or designed to be a industrial professional development system.