And me!
For sequels better than originals, I can think of several:
Hitman 2
IGI2 (already mentioned)
JK:DF2 (the sequel to Dark Forces, vastly superior--I won't argue the relative merits of JK:DF2 with JK2:JO)
Starfleet Command 2-only nitpickers could find things wrong with the 2nd vs the 1st
NASCAR Racing series--each is better than the previous, no exceptions
Rogue Spear
Most simple run-and-gun FPS, as there's nothing that could be left out without the game failing to load!
For me, the best examples of sequels changing with mixed results is the Jedi Knight series and the AvP series. In both cases the developer changed, however, so that's to be expected to a degree. The first AvP had no real story. It was barely better than the story in Quake.
I felt it had more atmosphere, though. The original SCARED me. Almost pitch black rooms, sudden loud noises, and DOZENS of Aliens running at you, combined with the weird fishbowl Alien view. The sequel was better in most ways, but lacked the sheer volume, and speed, of the Aliens in the original, and to me wasn't scary. Creepy, yeah, fun, yeah. Not scary though.
The Jedi Master