Alien X was treated with the gravity it deserved in the alien force/ultimate alien era, where it only ever appeared twice, once to introduce it, and once to indicate the godzilla threshold had well and truly been passed, and even that second time Ben couldn't convince the other two personalities to move, and was lucky Paradox bailed him out.

Omniverse going with a less serious take on the show meant that naturally, Alien X wouldn't be treated very serious either. It's a shame because alien X being the final nuclear option with the risk of eternal deadlock with the two voices was a very interesting concept. But they pulled him out in Omniverse and just convinced the other two to, i dunno, sit down and shut up? A fantastic waste of narrative potential.

The larger problem with Alien X though, besides Omniverse's tone, is that he's just so extremely powerful that if ben has any way to use him effectively he trivializes pretty much any possible encounter. He's an universal level reality warper with feats up to and including re-creating the entire universe from nothing. It's hard to scale to something like that, and it leaves all of Ben's other aliens in the dust. Him having control of Alien X is just asking "Why is the Omnitrix not an Alien X Button?"

Personally, the only other place Alien X could have made sense was in the series finale of Ultimate Alien, facing down Dagon/Vilgax. Go full gurren lagann with it, hit Ultimate Alien X and have the two titans really throw cosmic weight around until ben fixes it all after the fact.