I actually prefer The Witcher 1 and Mass Effect to their (direct) sequels, but I guess I’m in the minority.
I loved Vice City but I would say San Andreas blew it out of the water.
Also, fixing hammer-ons in GH2 was a huge gameplay improvement over the first game, although I still have a soft spot for the first game’s setlist.
Smackdown Here Comes the Pain (Smackdown 5 I think) was a huge improvement over Shut Your Mouth.
Also, SML2 Six Golden Coins was a big improvement over the first game.
Age of Empires 2 was a big improvement over the (already great) first game.