It's hard for me to say, I actually think most sequels I've played as of late topped the original.
However, one that does come to mind is Golden Sun: The Lost Age.
Around the midmark, or even later, it was best than the first one, but the beginning was awful.
You were just thrown in the middle of nowhere without any clue about what to do next and had to guess the order of events. Annoying. Then they re-did that, only worse, when they gave you a ship.
Just, please, stick to linearity.
Also, the Pokemon series has a bad case of this. Ruby/Sapphire were incredibly disappointing compared to Gold/Silver.