I have about 6,000 miles on a 2005 R1200RT and a 2006 R1200RT. Although I still prefer the appearance of the 2004 R1150RT, but the 1200 is superior in all areas of performance.
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 (BC) 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 2006. 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.
The R1200RT does burn oil. I assume it is like the R1150RT, wherein the latter stops burning oil ca. 10,000-12,000 miles. Interestingly, the 2005 burns more oil in the beginning than the 2006 -- could be some sort of change or just differences in individual motorcycles.
Both Cycle World and Motorcyclist named the R1200RT the "Best Touring Bike" of 2005. I see no reason to disagree.