In that case, the GTI is 'better' in the economy, looks, handling (maybe, depending on the weight penalty of 4WD), and tax aspects.
Of those, only two of those are a matter of fact, the other two are a matter of opinion. In the end only someone in the market for both can decide whether the premium of the R is worth it... You've made your opinion clear...
Personally, the whole experience of owning one of these cars is in how it makes you feel. A higher spec car with a few toys enhances the ownership experience rather than thinking 'I wish I'd have gone for ACC & Sat Nav' etc... I'd pick the GTI and load it up with options!
Again, you're entitled to that opinion; however, is there anything essential missing from the Golf R, yes adaptive suspension, sat nav etc. are nice to have but by not having them do they make the car that disappointing.
Many would have the opinion that £1700+ for the ProNav is daylight robbery - even £750 for the Discover system could be close to that when you can buy a more functional top spec TomTom for less than £300.
As for the adaptive suspension at £815... it looks like a lot of money when there was a thread on here not so long ago where many who had specified it could tell no difference between the modes and those without it are more than happy.
I'm not saying that those are my opinions but they are a valid alternative. Depending on a test drive (because to me it is how these cars drive that makes the difference, not the trinkets) I suspect I would take the R over a GTI specced up to the same price...
It is not a choice I will have to make for a few years because I got my GTD as a company car to save me money - it costs me only the benefit in kind (~£150 per month)
and saves me putting silly miles on my 996 Carrera 4S and the associated servicing and maintenance costs...