I would like to see a more advanced ("professional") Arduino IDE (I know I can use Eclipse).
This woudn't mean that the current IDE need to get more complicated for beginners, but if there would be either an additional "Pro Version" or at least some more features within the current IDE that would be fine. Some of my wishes would also be helpful for beginners, I think.
Some things I would like to see:
possibility to select and upload HEX and DAT - Files to EEPROM and ROM
Dump EEPROM to HEX File
Commenting functionality like in Eclipse
finding the method body if you mark a method call and press a special key (like F3 in Eclipse)
collapsing Code in the editor
I know there would be many more things - it is just a small example.
What about having the Arduino IDE loading "Plugins" ? So there could some tools be made by customers (like the EEPROM Dumper / Writer and an Hex-Editor to easily manipulate the eeprom hex file).