Hmm, the only ones I can think of off the top of my head are Final Fantasy Crystal Chronicles: Echoes of Time (as opposed to Ring of Fates), since it was a lot more flexible with creating characters, equipping items, and had a much less clunky way to handle multiplayer(although the original on the Gamecube is still my favorite), Megaman Zero 2, which had more hidden secrets and made it easier to get energy crystals, and Megaman ZX Advent (compared to the first), although that's mainly due to the fact that I played Advent first, and thus had higher expectations for ZX.
Oh, and Pokemon G/S and Crystal, when compared to Red/Blue. There are so many improvements, it's not even funny. (Real time clock and calender, events based on the time and day of the week, day/night cycle for finding pokemon, more organized bag system, seeing a TM's name without having to boot it up, graphical improvements such as color, inclusiou of the original Kanto region, the list goes on and on....)
Yellow was still pretty cool, though. Pika!