They could have included Omega Red. He could have been one of the Reavers like Lady Deathstrike was in the comics. Or he could have just been Rice's ultimate weapon and the source for the anti-mutant agent in household products.
The films have always taken liberties: Sabretooth wasn't a member of the brotherhood or Logan's brother. Mystique wasn't Magento's subordinate, Xavier's sister, or the template for the Sentinels. I could go on and on...
They put Donald Pierce in the movie and we didn't get his whole background with the Hellfire Club. We wouldn't have gotten Omega Red's background either but he could still have been an interesting and powerful villain for Logan. It was also the last opportunity to see this battle between Omega Red and Hugh's Wolverine which some fans have been waiting years for.