The manual box on my R is the only disappointment I have in the car.
It feels rough and gravelly, especially going 2nd to 3rd 4th to 5th and 6th to 3rd for some hard acceleration. It almost feels as though the cogs are rubbing slightly against each other as you are changing gear. It has been that way from day one, but seems to have improved a little very recently.
There are occasions where I've come to a stop in traffic, knocked it into neutral and let the stop-start kick in, only to find when I go to start up again that it doesn't seem to want to slot into first. I don't force it in that situation, I put it into 3rd with the clutch dipped, and then into 1st.
Similarly, dropping from 6th to 3rd it has happened maybe once a month, feeling as though if you were to force it, you would probably cause an almighty crunch
Happens far too irregularly for the garage to pick up on a road test. I bring the issue up every time the car goes into the garage for a service or warranty work, the technicians say that the "agricultural feel" is due to the box needing to be a bit basic to handle 300ps. A colleague's manual R has the same feel to it.
In 7 VWs and an Audi I have owned from new, I have never had a gearbox feel this coarse in use, previous boxes mated to TDIs have been far smoother, including the wife's current A1 1.6TDI.
I'm assuming the R's manual box is the same as that employed in the CS/CSS, but perhaps not the standard and PP GTI (which I am led to believe has slightly taller gearing than the R).
There are a few others here that have reported similar issues with their manual Rs.