I think part of it is that the MK7 Golf is a huge step up over the MK6, for Audi it's pretty much business as usual, although the MQB platform improves ride quality and handling for all. Within the VW range, the R is more special than the S3 is in the Audi range. The Golf is better value for money - it is so well equipped (it would cost you about £4k to equip an S3 to the same level).
If you buy an S3 SB/3DR over an R, you're buying it for the badge and the appreciably nicer interior, and you have the choice of the saloon variant on the S3. Some of the extra money is also undoubtedly going on the cost of the extensive use of aluminium in the bodywork.
The press always see the Golf as an affordable "peoples" car. The differences in set-up for mapping, electro-mechanical steering, damping etc are supposed to be negligible (someone who has driven both for an extended period would likely confirm), I always take reviews with a pinch of salt - they never seem truly impartial or particularly fair with their comparisons (like when they criticise a car with standard damping for it's handling, but it's up against a car with active damping technology, or they compare the 0-62 time of a DSG to a similar car with a manual box etc). They're both very good cars in their own right, with very little between them apart from the superficial (standard equipment on one, one of the best interiors you will see on a car under £50k on the other). Although Audi don't seem to put their money where their mouth is with GFV (56% for S3, 60% for the R), I do believe that actual trade-in values for the S3 will be a few grand better, which does go someway to offset the extra equipment you will have to buy - so many cheap lease deals available for the R should soften used values, there will be fewer S3s out there.
