I have the techinical documents on the EA888 engine design.
The reason they used the older unit in the R and Ed35 is simply cost. Design/homologation/type approval are very time/R&D man hour intensive and expensive financially, for such small production numbers of cars that would be sold in the life span of the mk6. They had a ready solution on the shelf they could use so used it, the older engine was the logical choice.
The Mk7 will be using a modified verson of the EA888 engine as the older engine will not meet new EU targets.
The modified EA888 engine to be used in the Mk7, will develop 220 bhp and has a modified valve lift system which is developed by Audi and also has other detailed tweaks.
The clock is ticking for a decision because the EA113 engine that powers the R and Ed35 cars is due to be phased out in 2014, ahead of new EU6 emissions regulations.
Sources say that the EA113 won't be re-engineered to pass EU6 regulations and instead it will be replaced by a high-output version of the current EA888 Golf GTI engine.