It's a tough one to compare to two models in terms of engineering.
I think you have been quite modest with that statement

Exactly as Dubber has said, the two cars are very different. It's not a case of driving them both until all four wheels fall off.
The argument for the Mk2 is that there are so many still around (however one must bear in mind that the "classic" status of the mark has resulted in many receiving far more attention than most cars of that generation).
The mk2 is a simpler car, both to drive and in terms of engineering.
It simply has less parts on it to go wrong. Whether one considers this lack of complication to represent a greater engineering is up to the individual. The argument for the Mk6 is the sheer
breadth of ability which the car offers.
Furthermore, the response depends on how you interpret the question.
Are you comparing the cars
directly? If so then one might argue for the Mk6 by suggesting that modern car construction is vastly improved, but equally so one might defend the Mk2 on the grounds that, as a simpler car, it has less to go wrong with it. It really depends on you're own personal appreciation of engineering -whether you are a 'less is more' or 'more is more' sort of person.
Or are you comparing the cars
indirectly - that is by comparing them to their respective contemporaries? This method may prove to be a better choice as it would give each car a context. The Mk2 GTI was without doubt, one of the finest (if not the finest) hot hatches of its generation. Class leading performance, practicality and German build quality established it as such. By way of comparison, the GTI no longer offers class leading performance and there are many German built rivals (even within the VW fold) which are attempting to steal the GTI's crown.
Which makes the more convincing GTI?Even within this question there isn't a clear answer. Fans of the original will advocate driving thrills, purity and performance. But in today's motoring climate the importance of the back road blast has dwindled. Emissions, refinement and ease of driving seem to be higher up the agenda. The modern GTI reflects such a change in attitude.
My own car is a completely standard Tornado Red GTI with only the DSG transmisson and Cruise control fitted as options. Even in comparative poverty spec (next to some of the cars on here),
the GTI remains the greatest car I have ever owned. It has travelled with me all over Europe, cruising with composure at speeds approaching 150mph. It has hauled everything I have needed hauled with it's usefully shaped boot and easily folding seats providing enough space. It has been relatively cheap to run, averaging over 40 mpg at best and low 30's at worst. It has set out with me from Motherwell, Scotland with excitement towards the Nurburgring. It has raced round, enthusiastically chasing far more exotic machinery, whilst looking after it's novice driver. And, having scrubbed it's tires, having emptied it's fuel tank and having sucked every insect in Germany through it's intake, it simply settled into 6th and carried it's driver - now weary and in need of rest - all the way home.
Sorry that this doesn't answer you're request, but hopefully it will help you in your work nonetheless.