So I probably wasn't alone in this one but I always thought that the final battle would involve Alien X being used as the last alien to save the day... or universe I guess, and I was right. First it was used by Skurd to make the sword, then a cameo by Ben during the rapid transformation sequence, and I can't be the only one who noticed that Skurd was Alien X after the Maltruant-makeover Annihilaarg was crushed by Ben. (He had a Celestialsapien arm). So technically speaking, Alien X did save the day after all. Skurd probably transformed into Alien X when the Omnitrix's failsafe kicked in, and most likely remained Alien X after Feedback destroyed Maltruant.
Still, I feel a little dissapointed that Alien X lost his specialty in Omniverse. When he created the universe, ok. Next in Universe vs Tennyson, Ben having control of him, ok. But Weapon XI Part 1 was just... nonsense. If he controlled Alien X he could have done so much more and pretty much, put bluntly, put all the battles that happened after that episode to a point where they never existed. At least Skurd doesn't have to deal with multiple personalities, but then again he didn't know that Ben had Celestialsapien DNA in the Omnitrix.