I had owned a 2006 MKV GTI and now 2010 (first year) MKVI GTI. I didn't/don't have 'boat loads of issues' you are referring to.
Though I did hear stories my VERY early build (10/05) MKV GTI was as reliable as one would expect. Not perfect (it is a VW) but was acceptable enough for me to buy another subsequent GTI.
The 'major kink' in the MKV GTI was that it was the first use of the 2.0T FSI motor which was the first production engine EVER to employ BOTH direct injection and forced induction in a single application. NOW, when they made the switch to the badged 'TSI' motor for 2008.5, they worked those things out. This new 2.0T will just be a further advancement of that.
It should, in theory, only get better the more time they spend on it.