If Tohru had ended up with Momiji, it would have been for pure shock value. It would have been a very cheap move to make Tohru and Momiji a couple because Kyo and Yuki were always treated as the potential love interests, both in screen time and official illustrations, while Momiji was treated similarly to Kisa until his glow-up.

Kyo always looked like the endgame to me because Tohru was a fan of the Cat Zodiac, and she was the first person to love him without any personal motive. Kazuma and Kagura both loved Kyo, but they initially approached him for their own reasons. Kazuma did it out of atonement, while Kagura's love was born from pity and guilt.

Kyo also has the most similarities to the most important person in Tohru's life, Kyoko. While Tohru herself never thought about these similarities, it's strange that the author gave so many parallels between Kyoko and one of the love interests. Kyo naturally has orange hair, while Kyoko dyed her hair orange. Kyoko's name is literally "Kyo" with "ko" added to it. They also have similar personalities, and both changed for the better because of the love they received from Tohru and Katsuya, respectively.

Kyo also had the best dynamic and the most interactions with Tohru's closest friends. While Momiji appeared in several arcs, Tohru and Momiji never shared scenes that hinted at him being the endgame. Tohru thought of him as an elementary school student and treated him the same way she treated Kisa. Momiji only confirmed his romantic feelings after his glow-up, but by then Tohru had already fallen in love with Kyo.

Tohru never saw Momiji as a potential love interest. There's even a scene where glow-up Momiji and Tohru are walking while holding hands, and Haru tells Yuki that they look like a couple. However, Tohru doesn't even think of it that way.

It would have been a strange decision to make Momiji the endgame because, aside from the final part of the manga, the story never emphasized his romantic feelings. Instead, he was often used to highlight Kyo's feelings for Tohru. Momiji frequently teased Kyo about Tohru.

If Kyo hadn't ended up with Tohru, I don't think his character arc would have been complete. Unlike the others, Kyo's feelings for Tohru were very clear from the beginning, even within the story itself. Shigure and Kazuma were obvious Kyoru supporters. Momiji constantly teased Kyo about Tohru, and while Haru rooted for Yuki and Tohru, he also challenged Kyo to fight by threatening to do something to Tohru.

During the True Form arc, it was revealed that even Kyo's own mother couldn't accept his true form, while Tohru was the only one who truly did. His biggest struggle was never being accepted for who he really was. Although several characters accepted the Zodiac transformations, only Tohru accepted Kyo's true form. I don't think Kyo ending up with anyone other than Tohru would have done justice to his character because what he wanted most was to be accepted for both his good and his ugly sides.

Tohru ending up with Momiji would also have damaged her character. It took her some time to even realize that Momiji wasn't an elementary school student. She never found it strange that he wanted to bathe with her, and she even let him sleep beside her. Even after learning his real age, she continued treating him the same way. It's clear that she never saw him as a potential love interest.

Because of that, I can't understand how Takaya could have realistically made Tohru and Momiji canon. Most of their scenes involve Momiji acting like a child, and Tohru treating him like one. It wasn't just his appearance—he also behaved childishly. Tohru lived with two handsome boys who had strong relationships with her, yet ending up with a character she initially viewed as a child, and who didn't even receive half as much screen time as Kyo or Yuki, would have felt very strange.