Most Sonic games after Sonic Heroes. Argue if you will, but I had fun with the franchise up to that point because most of the other games did some really stupid game mechanics I just couldn't wrap my head around. Some games were still fun, but failed at being good sequels to the series. Sonic Adventure 2 will probably be my favorite ever (and I know someone is going to flame me for that, but whatever, fuck them).
Other games I would say failed as sequels... Star Fox Command. This was reviewed as good by many, but I would say it was terrible. It tried to give total closure to the series (my theory is that Nintendo wants to focus on other games and put StarFox in the closet for now). It introduced game mechanics that also didn't really work and made the game less about what former StarFox titles were about. I could stand StarFox Adventures because it was like Legend of Zelda... but FUN. Armada and 64 are tied for my favorite because they both do a lot of things REALLY well. But Command just totally ruined this series and I hope they continue it because it was one of Nintendo's good ones.
Another bad sequel, but still an excellent game, is Metroid Prime 2 Echoes. Ridley didn't make an appearance. The Metroids were pushed into the background. Also, ammo limitations on beam weapons pissed me off. I get missiles and beam-missile combos having ammo. But why the fuck would you put ammunition levels for the beam weapons that we are forced to use for a number of things (doors, weak enemies, debris, crates, bosses, etc). Not to mention that dual-world gameplay wasn't too interesting either (granted probably some of the BEST level design in the series). Great game in a lot of respects, but not nearly as good as the original Metroid Prime nor Corruption.