Well, if a crossover with the Alien franchise is still in the picture, I think it'd be interesting to have the movie end with Royce and Isabelle successfully making it onto the Predator ship bound for Earth. They don't realize that in the ship's cargo area, the Predators have humans and Alien eggs in stasis in preparation for a hunt. Royce and Isabelle accidentally disable the stasis mechanism, and mayhem breaks out in the cargo hold as facehuggers attack the humans. Some people make it out alive and find Royce and Isabelle, and they try to hold out as Aliens infest the ship. Meanwhile, another Predator ship comes to intercept this one, but they can't blow up the vessel because of its defenses. Instead, the Predators signal Royce and Isabelle to let them dock, and they hesitate for a long time until they realize that they can't survive on their own, so a group of Predators comes into the ship to clean up the mess. The humans find a collection of Weyland Yutani weapons that the Predators took as trophies, including prototype pulse rifles and smartguns. Aliens versus Predators versus ad hoc colonial marines.
This is a sequel, of course, so the alternate ending could just have them entering the ship with a closing shot of alien eggs in stasis.