I suppose since I'm one of those people who've just come to VW from another marque and have ordered a Mark 6 GTi that I'm ideally suited to answer this question. It pained me a little to have to pay more for the GTi but I bought it for a few reasons over the Sciocco which, incidentally, I also loved.
1. I liked the look of the GTi more (admittedly that's a subjective thing)
2. The Scirocco only has 4 seats
3. The boot on the Scirocco won't hold anything significant without ponsing around putting the seats down.
4. I'd always wanted a GTi ever since I drove the Mark 5 at launch (was just never in a position to buy one of those).
So overall it's really just the practicality of it and (for me) the looks. VW are, therefore, very clever because they've effectively forced me into spending an extra 2 or 3 grand as they know full well the Scirocco is a compromise in practical terms for many people - in my case I didn't really have a choice as to which of the two to buy.