The initial biggest issues were with the MyFordTouch system and the DCT.
The MFT problem has, for the most part, been fixed. You'll have a few problems pop up here and there, but it's not longer a disaster like it was.
The DCT problem I never had, I think it's pretty good and I trust the reliability, but that's just me. I do know its not just a Ford exclusive problem though. The dual clutch tranny itself has proven to be faulty across the line, regardless of the manufacturer. IMO Ford has done a much better job than others at fixing this. (Took my GTI 4 months just to get the part in, communication was terrible and then they tried to charge me for it)
As much as people complain about the DCT, it is leaps and bounds more reliable than VW's DSG. VW actually got sued and investigated because the DSG was so horribly unreliable and quite honestly dangerous. My problems came on the highway at 70+ mph. (In their defense, eventually they caved and took care of those, myself included, that had problems through reimbursements and extended warranties)
The story behind my avatar: