Making the choice to not include Sabretooth allows the focus to stay on Logan, Xavier and X-23, and that’s exactly where it needs to be for the story that is being told.
James Mangold and Scott Frank made a very deliberate decision to keep the number of mutants in the movie very limited, and starting to create exceptions for notable characters could have easily created a bad “opening of the floodgates” situation that they didn’t want.
When viewed from the franchise perspective, this choice may wind up ruffling the feathers of a few fans – as the relationship between Sabretooth and Wolverine could have used a nice conclusion – but when looked at in the context of what Logan is, the decision does make sense.