Fix-It" of the franchise: 1. Ridley Scott had become disillusioned with the Xenomorph. 2. Damon Lindelof came along and muddled everything with his one-trick pony that attempts to create "mystery". 3. Fox wanted another franchise to milk money off of, so they allowed for a film that would require more explaining in sequels (a risky practice that will hopefully die away soon). You put those three things together, and you get what the final film turned out to be, a decent but ultimately unsatisfactory product.