Standard halogens on the R50 are rubbish - I ditched the perfectly good globes for +50's (50% brighter) and never looked back. Mind you, it needed 6 globes (low beam + high beam + driving lights) @ $30 a pair.
Comfort Access on the early R50's was programmable by the dealer. Mine is default programmed to just pop the boot, but can be programmed to do other stuff (activated by pressing and holding the unlock button for about 5 seconds). And in the early days (quickly removed from the option list) if you also had the phone kit and climate control, and the car was in neutral (or park in the autos) you could SMS it to start the engine and run the a/c or heater before you got to the car.
Haven't heard anything good about the R56 stereo. IMHO I went for an aftermarket equivalent to the Mini SoundModul. Can't go wrong with 880 chunky watts of digital sound....
I reckon the biggest thing about all of the Mini options (ever since the R50 was released) is that it all comes down to personal choice - your Mini will be built as YOUR Mini. Not for anyone else. With your options. Even if others wouldn't have chosen it. You might need to spend some time in the dealership (I spent several lunchtimes with mine before ordering

)