Tough choice. Both AvP films were pretty terrible, but they are also easily dismissed from the canon so they don't do any real damage to the franchise as a whole. Alien 3, although not a terrible film, was where things started to go wrong. As much as I love Ripley as a character, I think she has become something of an albatross around the neck of the franchise, they were so scared to make a film without Ripley that they took the story in directions that it probably shouldn't have gone in.
This was one thing Predator 2 did well, by starting a whole new strand of the story without Schwarzenegger they were free to take a whole different approach free from the constraints of existing characters.
Ultimately though, Aliens Resurrection was, for me, the sequel too far. The huge time jump and the inclusion of Ripley once again both contributed to making this film the weakest of the main line Alien films, and therefore my choice for this poll.