I haven't played Shift 1, and I know only bits about the features in Shift 2 but...
Pit stops
Flags
Safety car (Wiesmann GT?)
Tyre wear, punctures, damage
Fuel load, fuel consumption
Qualifying
Mechanical damage
Dynamic Weather (rain, fog, etc.)
Endurance races
Penalties
Grid girls (Why not? It's Need For Speed afterall)
Racing teams, sponsorships, liveries
Online leagues, teams
The stuff in bold, Shift 1 already had. Admittedly, the damage was optional, and a lobby creator couldn't mandate it (hope that's fixed!), the penalties were just for track cutting, and weren't completely effective (mind you, GT Academy is showing just how bad PD got that, too) and the online leagues and teams, you had to organize for yourself (but they did patch in a whole Team Racing mode, where you automatically got assigned to Red Team or Blue Team - it over-rode your livery and painted all team member's cars the same - and then you won or lost as a team).
There was MUCH in Shift 1 they got right. Only the physics let them down, and, to be perfectly honest, after seeing Shuffle Racing in GT5, with everybody hooning around on Comfort Soft's, I don't think it's half as bad as everyone made out!
Shift's idea of an Endurance Race and PD's is a bit different! Shift's idea of Endurance was three laps of the Nordschliese, GT's idea is you sitting in front of your PS3 for 24 hours without being able to do a save! I don't think either of them got it right, at least in regards to a GAME! But you COULD specify a high number of laps in an online game if you could get anyone to race it! Few would...
At the moment, we are waiting to see if tires and fuel are depleted. I will be saddened if they aren't. Word is, no pitstops, but this being a game, you don't REALLY need those. Just the wear, and then pull off the track and hit the 'refuel and re-tire' button, and have to wait it out. We'll just have to wait on that one.
Qualifying would be good, so would flags, at least for start and finish. No idea why, if they went to the trouble of modeling flag girls, they couldn't be bothered with a green flag and a checkered. Laziness...
Yellows, double yellows, etc.? Only if they don't remove track debris (they didn't in Shift). Personally, I'd rather they just made the obstacles go 'poof!' as this is a game..!
Some good stuff there, though. Keep 'em coming, everybody.