Aliens and Predators. I Love Aliens, and I love Predators... but everyone who has every brought them together, bar AvP games (not the recent one) has laughed in the face of the lore. In fact, they laughed so hard, they created a lore of their own.
And that lore is fucking retarded.
Can't wait to see Prometheus to see how Scots reverse continuity works out. I liked Predators evolution of the Predator Lore... but the AVP films were just painful, either making Predators too wussy or completely ignoring established Alien biology.
EDIT: And don't get me started on the Comics. Those things were just horrid... like piss poor fan fiction with a small budget behind it.