I haven't played the game, but I know what's in it, and what's not. While generally improving most aspects of the game, Rockstar didn't keep some of the most original things, such as:
-buying more safehouses (only four in the entire city?!)
-car/clothes customisations
-bicycles
-more weapons (I personally miss the minigun and flamethrower)
-airplanes (they were kinda hard to steer in SA, but still fun)
-parachutes (one of the best things about SA were that you could go free-falling off tall buildings or planes, and survive it)
-the 'funny' weapons (dildo, vibrator, flowers)
-Ammunation (it was a great symbol of America's love for guns)
-the stretch limo always looks kinda crappy compared to the other cars, in every game
I didn't care much for the motorbike missions and stadium stuff, but it apparently there isn't enough to do in the game without them.
And this isn't 'missing', but I think it would have been cool if the environments were destructible, even if it was only certain buildings.