Pretty much bang on there monkeyhanger. No matter what the owner buys, they will be happy with it, period, because it is right for them. How much financially better off you actually are with one over the other will vary greatly depending how long you keep it, how many miles you do, how you drive the thing etc. I did the maths on a spreadsheet and yeah, if I forget relative depreciation because I plan on keeping it, the extra per year in fuel and tax for the GTI was an insignificant few hundred quid a year. Insignificant in that it equates to just over one monthly payment of my three year loan for the car, which will be paid off either on or before the end of the term.
I also have a GTI right now so the fuel costs are going to be lower, if not by much. On the whole I don't go caning it around, and accelerate quite gently most of the time. I prefer the GTI, being blunt, for its red accents! I also prefer driving a smooth petrol engine, although I grant you that modern diesels are very, very good. For me though, it's not about outright acceleration, top end and torque, or indeed economy.
As for exclusivity, I'm obviously biased but can see both sides of the coin. In a way it makes it more exclusive because there are less of them on the roads. I guess in terms of desirability, you can look at it two ways as well - either it's not what people want these days, or they do, but just want obvious lower running costs, as significant/insignificant as they might be.