The worst sequel of all time has to be:
Deus Ex: Invisible War
Held back technically due to the technical limitations of X-box 1, completely dumbed down for a console audience but ruined the game for both audiences, removed the vast majority of RPG elements and had characters that just didn't feel right. You could kill one characters wife and they'd say one line and give you your next mission... wtf?! Couldn't believe how such a great game as Deus Ex could have spawned such a piss-poor sequel.
Other than that:
MGS2
MDK2
Empire Earth 2 (and 3 which was even worse)
Modern Warfare 2
Call of Duty 3
Tomb Raider: Angel of Darkness
FFXIII








