Wild ARMS comes to mind, largely cause they balanced the characters out really well whereas the sequels always made it so one character was a crutch character and the rest of the party was backup. While Wild ARMS 2nd Ignition brought in some cool ideas and has better writing, I still feel WA1 had a better story cast, and overall design.

I would probably second Final Fantasy Tactics, while I did have fun with the TA series, I have issues with both games pacing and gameplay, and while Tactics isn't exactly perfect in these departments either, I can live with how they did it whereas I find TA1 and 2 to be very grating. TA1 has a great story but I don't feel it hits as many points as Tactics and I felt Tactics had a more profound ending. TA2's main story is the game's main weakness.

Beyond that, this is pretty tough, I'm sure I could think of a few if I thought of lesser titles where the sequels were quick cash-ins and largely just felt like extensions of the first game, but actual legitimate sequels is a bit harder. I can think of a few games where the second or third entry in a series that goes into double digit sequels often is the best entry and beats every thing after it.