My problem (in the real life!) has always been judging the break properly. I think the mesh that the game applies to the green with some small dots moving faster or slower according to the break is really helping and once you know how to read that it's not impossible to imagine something similar on real greens.
I might be talking but rubbish my putting has been excellent for the last five rounds and the green reading above everything. Obviously once you've read the green you need to be able to play the shot you want and the game can't do anything about it.
It might not be complete rubbish - there was an article in (I think) last months mag where one of the coaches suggested visualising a T shape on the green not dissimilar from the grids on the game
I don't play golf on the pc any more but when I did I'd read the greens exactly the same way that I do on the real course by trying to visualise the ball rolling to the hole and how it would be affected by the slopes.
Maybe it's helping your visualisation skills which in turn helps green reading?
My mate told me that my positioning when I played defensive mid had improved since I became addicted to playing the position in FIFA 10 for the PS3... I told him he was being ridiculous, as admitting that would've been too sad to take but deep down I knew he was right...