I know a lot of people say the rear camera is pointless, small hatchback, blah, blah... but having had it on 2 MK7's, I would NOT be without it. One of the first options I'd tick. It's a brilliant convenience, I'd lose the sensors before I'd lose the camera. Maybe I'm just sh!t at judging the car when parking but I find it invaluable, giving you an exact visual of where the bumper and the wall/obstacle is.
Other than that, I'd have to have:
5 door
19's
DSG
Keyless (another option I am used to now and would not have a car without it).
After that it's into "fripperies".
I have leather in the R. I think a car in that price bracket needs decent seats and the R's cloth seats just don't cut it IMO (I know I know, the VW leather is not brilliant but it looks far more premium to my eyes.). If there was a nice half alcantara/leather option I'd choose that instead though.
I have Nav in the R too and tbh I rarely use it. I could live without.
I don't have DCC but I'd be tempted to try it next time.
Same for Dynaudio.