The changes from 2005 to 2006 in the R1200RT are pretty minor.
The colors are the same (alas, no Biarritz blue).
The illuminated red emergency flasher button on the left handlebar is gone. To engage the dual flashers, you press simultaneously both turn signal buttons. The ambient temperature indicator in the LCD, if you have the Bordcomputer now reads accurately, whereas it read 5° to 10° too cold on the 2005 models.
In order seemingly to lower the MSRP, BMW Motorrad USA has made a lot more a la carte. For example, cruise control and heated grips are now options! Moreover, you only get one metal key and, effectively, no tool kit -- the latter ending an 80-year long BMW tradition. It's a shame that you do not get two keys and a tool kit on a motorcycle that approaches $20,000 U.S. out the door.