Interesting question.
I've done the same recently, with my current RS (RS162) wagon, GolfR Grid, Superb 206, and Tiguan 162.
Ultimately, what do you want from the car, and how much are you prepared to spend?
GTi: I would say delete this option. As you've mentioned, there is a price premium, for effectively the same engine/running gear as the RS245, but in a much smaller car.
R: IMO, not worth the price hike, over the RS245. As you've mentioned, smaller car, even though it's the wagon version and has bigger boot space than the GTi. But there is a weight disadvantage in the AWD system, even though this is assisted with the extra performance.
The extra engine performance in an R (or a Superb206) isn't JUST a bigger IS38 turbo/tune, the internals apparantly are also different/stronger, so that's a plus.
Overall, I personally think you're better off with the RS. Bigger room, all the trinkets, but yes, you miss out on the nice virtual cockpit, but in reality, it has a massive satnav/info screen anyway, for showing your navigation, etc. The digital dash thing is just another thing to go wrong in the future.
BUT - the crowning glory is that ALL 3 options are easily tuneable/upgradeable for pretty little outlay, if that's your intention.
A simple JB1 or JB4 will bring the RS to a completely different life - but then you're looking at struggling to get the power to the ground. But that's the same situation with the GTi.
The R can also have the JB installed for extra performance, but as you've mentioned, overall, it's almost 50% dearer than the Skoda.. and for what?
Plenty of people have swapped the Skoda/GTi turbo for the bigger unit from the R, or a hybrid, or simply tuned it properly and a few tweaks to suspension & wheels/tyres, to get almost the same performance and much better handling than an R, considering the weight disadvantage of the AWD. Plus the fact the Haldex units are notorious for failing and being expensive to maintain.
Lots of questions for you mate...... but ultimately, what do you want from your car.
Comfortable, roomy daily cruiser, which can be very cheaply tweaked for better performance and handling = Skoda
Compact daily cruiser with a digital dash, which can be very cheaply tweaked for better performance & handling + $4000 extra cost = GTi
Middle-sized balls-out thrash machine, which can also be cheaply tweaked + $18k extra cost + the "R" badge & associated street-cred = R wagon.
Compact balls-out thrash machine, with no frills, no nice seats, no fancy bits, and no boot space as it's the same as the GTi + similar cost = find a Grid R.
OR - in reality, find a cheap 1yr old Superb 206.
All the space you could ever want or need.
Still 4 years warranty.
SAME engine/turbo/power/AWD running gear as the Golf R.
SAME upgradeability as all the others.
ALL the trinkets of the others, except the digital dash I think.
$$$1000's of savings over than "R" badge on your keyring.
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