The blue issue - I'm happy for the R to keep Rising Blue, I'm thinking the dark blue they have on the Polo GTI as an alternative.. if nothing else it keeps with the dark conservative choices GTI buyers seem to pick. The show car blue might just be too crazy for us otherwise!
3 door/5 door - I don't see the problem in keeping a 3 door option for those that want it.
Manual/DSG - keep a manual option for those that want it. Seems like it won't be long before this might be a real selling point.
Again I understand that for stock ordering/control/costs its best to keep options and choices to a minimum, but given the factory produces these options and so long as the buyer is ok to possibly wait 6+ months for a special order.. just allow it.