There aren't that many sequels that have really let me down. Most sequels I enjoy. Super C and Mario Kart 64 disappointed me the most, but those don't have "2" in the title.
Here are a few titles that let me down:
God of War 2: The gameplay was there, the story didn't interest me. I mainly just screwed around and zoned out through a story I didn't care for.
Metal Gear Solid 2: Same as God of War 2. Playing the game wasn't bad, but the characters and story weren't very interesting. Plus, it seemed like there was a lack of boss battles compared to 1 and 3. Metal Gear Solid games are all about bosses for me.
RPG Maker II: I really enjoyed making screwy games for the first RPG Maker. There seemed to be less options and less screwy enemies and characters in the second one, thus I could never make an "Angry Donkey and the Legend of the Barnyard Warlock" sequel game for the sequel.
Kid Icarus 2: Disappoints me by not existing. Maybe I should have made that with RPG Maker II.
Those are the only ones that really stand out. I've suffered other small letdowns, but nothing major. I've also suffered some bigger let downs on sequels past 2.
I didn't own any consoles during a large part of the Playstation/Saturn/N64 era so that might have saved me from a few disappointments. Also, I never had a Genesis as a kid. Growing up a little poor and not buying a lot of sequels probably helped me not be upset at bad sequels.