I've been doing a little initial dabbling in Arduino tutorials in preparation for an upcoming project that involves (gasp) actual hardware, and as usual my thoughts continue to want to make it all a new domain. What I'd really like to see is a single specification that defines the circuit on the Arduino, the code running in it, and any UI code on the host that talks to it (whether through the serial port or by radio).
Those pieces would then draw the schematic, write the Arduino Java code, and write the host-side C or Perl or whatever is running over there. Later, you could even automate the assembly of the circuit on the Arduino side (wouldn't that be a cool project? Combine it with the circuitry evolution thing I saw a couple of weeks ago....)