Say money wasn't an object, what do you think would go quicker with enough work? Not changing it so much it's not the same car, if you get me.
The Mk6...it has an engine capable of far more power and a vastly better chassis.
Modify a Mk3 and you can make it quicker - in places - than a Mk6 GTI...but that Mk6 will be either standard or mildly tweaked.
Take the Mk6 to a similar level of suspension tuning (camber adjusted for example), better dampers etc, add a LSD, up the power and the better chassis will show. The Mk6 will ultimately be the faster car...ultimately the difference in weight is not enough to offset the vastly better chassis on the Mk6.