Might and Magic IX - Went for eye candy over game play.
The third Krondor game - More eye candy, virtually no game play.
Thief 3 - "Consolized" the game. Missions were composed of several small linked play areas instead of large rambling areas to explore. This was done to adapt the game to console hardware limitations.
MOO3 - An example of change for its own sake. Did anyone actually like this game?
Wing Commander III and IV - Examples of challenge disorder. There were too many missions in these games that were virtually impossible to beat, and the dynamic difficulty setting system made it impossible to adjust the games to your personal skill level.
SimCity 2 and later - Added too much complexity, ruining the game experience. Remember: KISS!
Civ3 and 4 - More challenge disorder. Even at the easiest difficulty settings these games are very hard to beat.
There are more, I am sure, but I'll let other Slashdotters come up with them. And yes, I am aware that many people enjoyed many of these games but, speaking from my own knowledge (from conversations with other gamers), each of the games I have listed lost a large part of their audience, with only the hard core fans of the franchise claiming to like them.