I remember reading somewhere that in VW's patents for their GDI engines, they did note carbon build-up is an issue. Needless to say, a lot of RS4 owners were pretty pissed to be losing anywhere up to 30-40hp at the top end after only 20k miles.
VW engines certainly aren't the only ones with this problem though. How manufacturers will address it seems to vary a little bit. The current generation LS engine (LT1) is now direct injected. GM claims their PCV system has been redesigned to mitigate carbon build-up. As Will pointed out, Toyota (e.g. the FR-S / BRZ) use dual injection to solve it. VW is also now using dual injection (e.g. in the current EA888).
All fine and dandy for future iterations, but for folks like us we're stuck with the problem. From what I've been able to gather, air-oil separators don't help. Water/meth injection seems to prevent additional build-up but won't really clean away anything that's already there. The only thing you can do is pop the intake manifold off once in a while and clean away.
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