I think the Arduino is brilliant as is.
Please don’t change a thing. Please don’t even be tempted to seriously consider changing anything.
Featuritis (adding cool new features) is a disease and IMHO ‘improvements’ to Arduino risk killing it.
I don’t know whether you guys designed in or stumbled upon the secret for a beginner’s microcontroller, but the system ‘as is’ is genius.
Steve Jobs also possesses this secret and is somehow able to resist the temptation to add features to Apple products thus keeping it usable by the masses. Those of us who know a lot about embedded systems don’t need any additions, we have other tools, those who are just starting out don’t need to be distracted by adding any clutter.
I’m fully capable with advanced tools, but I use the Arduino all the time for quick checks on hardware prototypes. Firing up AVRStudio/WinAVR and AVRDude is a hassle and I’m glad to have a simple short cut.
I know that a lot of threads get started by folks who exhaust what the Arduino does easily and they want various changes - but IMHO they should move on to other tools and let the Arduino serve its original purpose as a platform for novices and for tinkering.