In looking for my first GTI I have been holding out for a 6MT, but have noticed the DSGs are trading at $1-3k less than MTs.
First off, nobody can explain used car prices right now, our economy is playing crash bingo. After having my 6MT for nearly two years, I can say I am over the phase and wish I would have went with DSG. If you are looking for a used car specifically, a DSG gives you the peace of mind of knowing some kid didn't money shift it, wreck the clutch, or hoon around town at 5500 RPM. I guess you could still do those things in a DSG, but I would argue it's less likely.
The DSG appears to be smoother and faster, and will give you a chance against the 10 speed evolution of street-racing cars that are all over the streets today. The 6MT clutch will need to be replaced some time after you go stage 1. The DSG stock clutch pack tends to hold up for a while longer. The only thing you will be dealing with is the DSG service, which will run you a pretty penny if you don't have the means to do it yourself, or a private mechanic that you are good friends with.
Still, at the end of the day it's going to come down to what you want. If you
need the interaction of a manual transmission, what can anyone say that will change your mind? Make sure you pick out a stage 3 clutch ahead of time.
edit: I just finished my full short shifter setup and may have completely changed my opinion on this.