Yeah Skyline in general is better for racing, but so it should be, its got race heritage and a racecar look. On the other hand the Supra was produced more as a 'Sportscar' for highspeed highway cruising and smooth (with stock turbos) suburban driving. It just happens to be very very quick for quite a small price.
I must admit you would get a bit mislead if reading about Supra's on the net simply because most of the information about them is from the US. The locally delivered US model has more power than its JDM twin and in general is easier to tune (i.e. before doing more major upgrades, single turbo's etc.).
Personally it would depend what i wanted the car for. If i had the choice and i wanted a sexy, fast and extremely cool cruisin' car (just look at that c0ckpit-like interior!) i'd go a Supra. But if i wanted something more of a weekend track warrior and day to day quick car with presence and heritage i'd go a GT-R.
Apart from that most of what everyone has said so far is true in terms of validity and personally i just cant decide which car is 'ultimate' in my opinion.