I haven't really read through the thread but I've read the OP and I'd like to add my two cents. I'm not a racing driver but I don't consider myself a poor or inexperienced driver.
1: Lift off oversteer. I'm sure this dead horse has been beaten a million times before, but I'm going to mention it again. Lift off oversteer was the only thing in real life that GT didn't prepare me for. When induced purposefully it's quite fun, but when it's unexpected it's important to know what to do. I nearly spun my parents' car (Honda Fit, 2nd gen USDM) on a very cold day when I lifted off mid corner to avoid understeering wide. The back end stepped out, and being used to oversteer only happening on a rear driven car in GT, I lifted off the throttle while overcorrecting and the back end swung the other way. I did get it under control without leaving the road or causing any damage, but it was the only time that GT's physics trained me poorly in real life. Obviously I'm not blaming GT for the incident; the fault was purely with me and my poor and immature driving, but I feel that if GT did implement realistic lift off oversteer I may have been better equipped to deal with the situation and even make it into a fun corner.
2: The sensation of speed. Again, it's been said. And this is much harder to implement in a game, I grant you. Wehnd riving at 80 mph down a tight country road, you feel as if you're going very, very fast. Even when you're doing 70 in a kart on a wide kart track, it feels incredibly fast and thrilling. In GT, anything below about 120 seems to feel fairly sedate. Part of this is because one is usually on a racetrack with few reference points, yes, but the vibrations and seat of the pants feel of speed isn't there and can't really be replicated. When I raced a Club 100 kart (2 stroke, about 75 mph top speed), the constant vibration in the chassis as a result of the engine was as wearing as anything. That's something GT will never really be able to replicate cleanly.
3: The satisfaction of shifting. This one is really just a budget thing; if I had more money I could buy a shifter and three pedal setup and have a more realistic setup, though for that money I could just buy a car. I find that the best bit of driving is the satisfaction of getting a shift just right when going into a corner. A perfect heel-toe is a great feeling, and GT isn't really able to replicate the mechanical joy of operating a car. I suppose it's not just shifting; the overall sensation is lost because it's being simulated rather than created physically.
That's pretty much it, really. GT is a surprisingly good learning tool when the above is accounted for, and it's still a great game regardless of how much whinging people do. And yes, I realise all those things have been said before many times, but I happen to agree with them.