A few other games that fit in with your theme of changing stuff up in a sequel:
Street Fighter,
Legend of Xanadu,
Resident Evil from 3 to 4,
Ninja Turtles,
Alundra,
Panzer Dragon from Zwei to Azel,
Actraiser,
Ogre Battle to Tactics Ogre,
Shadowgate,
Double Dragon 4 to 5
I kinda think that you can put pretty almost any game that had its roots on an earlier console and then made an appearance on the PS1/Saturn/N64 era or later systems in these sort of lists. Off the top of my head:
Metal Gear,
Zelda,
Mario,
Shining Force,
Metroid,
Sonic The Hedgehog,
etc