Reliability wise, the GTD seems more solid than the R or GTI (drivetrain-wise). There have been many GTDs chipped or boxed up to the region of 240ps/500Nm with no ill effects. On the other hand there have been more than a couple of buggered Turbos and slipped clutches on chipped/boxed GTIs/Rs and even standard Rs - the 2.0TSI engine and clutch don't seem to like more than 300ps going through it.
5 door is more desireable on the used market, with someone buying one new and selling after 3 years will see almost all of their money back in higher p/x prices for 5 door over 3 door. Most people want 5 doors in a car the size of a Golf these days.
Front suspension mount bearings were an early cause of concern on the first GTIs and GTDs coming through in mid-2013, but most of that was down to dealers leaving the transport pucks in at PDI.
Real life mpg depends greatly on your daily commute. The MK7 GTD takes a lot longer to warm up than older TDIs, and it's thirsty when cold:-
5 mile journey in Winter expect under 40mpg, in Summer expect 42mpg
10 mile journey in Winter expect 42mpg, in Summer expect 46mpg
20 mile journey in Winter expect 48mpg, in Summer expect 52mpg
50 mile journey in Winter expect 50mpg, in Summer expect 55mpg
For really long motorway journeys cruising at 80mph, expect around 58mpg in the Summer.
Those figures are not driving like a nun and on free-moving roads in a manual GTD. DSG are a little thirstier, and if you're stop-starting all the time through a traffic light riddled city centre on your commute, expect less.