VW chose the EA113 over the EA888 for the Ed35 for a reason! Brilliant unit. Check out the Car magazine Sports Car of the Year feature in which the Ed35 beats the 1series M, 370Z, Mini coupe JCW, RS3, DS3 & comes joint second with the Megane Trophy, losing out only to the Cayman R.
Which you think is the best unit depends on whether you want 2 or 4wd. Personally it would be the Ed35 for me. I love the unit in my Mk5, and will skip the standard Mk6 based on a recent test drive which confirmed what Car says in this article; "using the EA113 unit........the rawer character so far missing from the MK6 GTi is back"