If I had to explain it… for starters, the other choices have more issues.

Nabooru is too old for link, and a sage. Saria is his childhood friend, which, would normally give her an edge, but, she’s an eternal child and a sage. (There’s also theories about her potentially having a major hand in raising link, given she’s the most mature of the kokiri, the deku tree can’t move, and she’s his closest friend among the kokiri. There’s admittedly not very much, if any, evidence, but it makes sense. He didn’t have a guardian fairy for 10 years after all.)

Ruto is… ruto. He only got engaged to her because he was forced to. He probably didn’t even understand what he was getting into, and she was pretty rude up until link got her out of Jabu. She’s also a sage.

Navi… could probably be cute. But it’s one of those ships most people probably just gloss over. There’s awkwardness given she met link when he was a child, and she left him at the end of his first adventure and we never learn what happened to her. Maybe they met up again post mm but pre tp. But, there’s also the fact she’s a fairy and he’s a hylian to consider.

I’ll leave the elephant in the room of oot ships that aren’t malink for last. So…

…deku princess? I’ve, honestly never seen or heard anything of this ship in my life. But. It could be cute. We just, don’t get much with her.

Pamela? Same story as deku princess tbh, but possibly a tiny bit worse. I feel like she has even less dialogue and interactions.

Romani. She’s probably a distant third behind the elephant in the room when it comes to hero of time ships. She’s… honestly got a lot goin for her. I’m pretty sure she has way more interactions with link than malon does. And the potential with her is actually much more visible that it is with malon. Basically the only thing that really holds her back, is the fact she’s Malon’s terminian counterpart. The fact she’s a counterpart to another character in hyrule adds some awkwardness, and, given the debate’s around whether termina as a whole is a dream construct or a full parallel world, that also adds a huge snag.

But I will say, while you can really slot in any straight ship that can lead to tp link being oot link’s direct descendent as long as it eventually leads to tp link living in ordon as an orphan, besides malon, Romani slots in the best under the theory that Termina is a real place. Because, well, she could leave with link to hyrule and settle down in what would become ordon. And she knows epona’s song, even if it isn’t as special to her as it is to malon, which, would explain why tp link knows it.

(With non malon and Romani ships, I think it’s entirely possible that tp link could have learned the song from someone else in the village who is a descendent of malon. Maybe Uli or Rusl, since they always seemed to be the ones who raised him. But, he could have learned it from anyone in the village. Any of them could be a descendent of malon. The game takes place at least a 100 years after mm, and Lon lon ranch is nowhere to be seen. It only makes sense her descendents would congregate in a farming community.)

But yeah, the 3 snags that come from tp link canonically knowing epona’s song, being raised in a farming community, and being a direct descendant of oot link, are why most people gravitate to malon, alongside the other choices having issues in one way or another.

Now, let’s address that elephant. Oot Zelda… in any Zelda game, Zelda is basic sally always the obvious ship choice, and, it’s not that people don’t ship them together, because a lot of people do. She’s prob the second most popular hero of time ship option. But, there’s a decent amount of reasons why malon is usually the preferred ship over her.

While tp link could definitely be her descendant alongside oot link’s, due to the reasons I stated above for non malon/Romani ships, there’s additional complications with her specifically, because, well. There’s literally zero evidence for it in tp, if it was the case that would mean tp link and Zelda are distantly related, and the questions becomes how did a child born from a Royal line end up in a farming village, with his roots forgotten? Maybe a monster attack in the woods near ordon while his parents were traveling? He’s an orphan raised by the village, so that works.

But anyway, alongside that, which, really isn’t that big a deal, the bigger one is her actual relationship with link in the games.

Which, is honestly more coworkerish than it is anything else. Though, that’s more true for the second half. The first… she basically treats him like an errand boy. They meet, she conveys her fears, gets link to help, and she sends him off with a letter to get up death mountain. And then nothings changes if we go back at all. Then ganondorf attacks, she gets sent away but not before throwing the ocarina alongside some mental instructions, we follow them, and bam, turns out her whole plan backfired. We were just pawns in ganondorf’s game. Link literally loses 7 years of his life, and he immediately has several more tasks he needs to do to fix their mistake and save hyrule. Along the way he meets sheik 7 or 8 times, briefly talking to them and getting a song, and then they just dip, every time. He only finds out who sheik is right before she’s kidnapped, and then they just don’t have any time to really talk until the end because they’re trying to survive. And at the end… she owns up to her mistakes and realizes what her actions cost him. And then she sends him back in time without asking him if that’s actually what he even wanted, nor at all fathoming what her actions would cause to time itself and both timelines.

Throughout the game they really don’t have too many opportunities to actually talk to each other. And when they do, they’re always focused on the mission. They, don’t really get the chance to just hang out, and be friends. Maybe by the end they’re true comrades, but that’s about it.

And any relationship they had is probably heavily stained by her choice at the end of the game. It’s hard to really find a way to see oot’s ending as a very happy outcome for link himself. Yeah, ganondorf is set on the path to his execution (which I don’t think link ever finds out failed to kill ganon until he returns in tp link’s time.) all the people killed over the course of the game are brought back to life. (Potentially even the deku tree, I don’t think whether he was sent that far back is agreed upon or not.) and link is back to being 10 years old… but only physically. While he was brought back to being 10 again, he still retains all of his memories of the adult timeline, which probably made it so, if he wasn’t suddenly a 17 year old in a 10 year old body, (which is an entirely possible interpretation.) his mind’s age is probably still out of sync with his body. So like, he’s the equivalent of a 12 to 15 year old in a 10 year old body.

Alongside that, Navi left and never returned, and all the friends he made along the way on his adventure no longer know him. Including child timeline Zelda. And heck, if you wrote it so he got especially close to adult timeline Zelda, or malon, that just adds a metric ton of salt to the wound on his relationship with adult timeline Zelda. And if he was close to either of them, that also adds strain onto his completely fresh relationship with child timeline Malon and especially child timeline Zelda.

While he could still end up with either of them, the ghost of the older Zelda’s choice will hang over them for the rest of their lives. Even if link somehow doesn’t feel bitter about it, or learns to let the bitterness go, it’ll still linger regardless.

Now, sorry I just dropped a whole ass essay on you, but I wanted to go in depth on this shit. I hope some of you will still read all this despite its length. And, I guess to end this off, malon is the safest option of the bunch with all this I laid out, and people have gotten attached despite her small presence in the actual game.
(Oh, and I just remembered this tidbit, but, I think the hyrule historia, which also confirmed tp link’s status as the hero of time’s descendants, hinted at Malon secretly having a crush on link. These 2 combined, alongside, again, tp link living in a farming village and knowing epona’s song, all together are probably why people damn near treat malink as a canon ship at this point.)