For starters, Hajime Isayama could just have him not end up with anyone.
and Also, I don’t recall him actually saying directly that he wouldn’t make Mikasa and Eren couple.
The closest I saw was when he said there would be a separation between Eren, Armin, and Mikasa where they sort of oppose each other, and also when he said Mikasa’s presense is more like a mother to him rather than a lover, as well as saying Eren will eventually move away from Mikasa once he grows up and becomes independent from her like towards ones actual mother.
Only, things could still change later next time they meet, and it’s questionable how literal all this is.
Nevertheless, this could still be evidence that he might not intend to make them a thing. In that case, if we’re being unbiased and going by logic, I feel Historia would be the best bet for him. I really like Historia x Eren and feel that relationship is underrated overall, both in terms of the love it gets from the audiences and the logic and likelihood it has to be. Besides maybe Mikasa x Eren and supposedly Ymir x Historia (the main 2 relationship overshadowing it), no other relationship is more logical to actually happen for either character at this point.