It should be Zelda.

1. Zelda needs to accept responsibility for Hyrule going to hell so often. Hyrule has fallen about a dozen or more times? I mean,it makes Zelda seem pretty incompetent as a monarch. If Zelda and Link are together,that could open up new ways of fighting or problem solving. Zelda is more of a magic user,Link is more of a fighter. Maybe they come across an obstacle that neither can budge or destroy,but maybe combined might can defeat the obstacle. Zelda needs to see what her shoddy leadership had done through the eyes of her people. And she needs to fix it.

2. Closure. It is usually either Ganon or he is in the background that causes the strife. Don't you think Zelda would want to punish Ganon herself? And this way she proves her right to rule over her subjects.

3. The Ivory Tower. Zelda usually has had a sheltered upbringing. Wouldn't it be good for her to see other ways of life,to appreciate where the stuff she has comes from,to see the world beyond her castle?

I think Link oughta be paired with Saria.

I guess I should point out that I'm not a hyper Zelda fan, and I'm only really familiar with pre Twilight Princess Zelda hands-on (though I have played some spin offs and not unaware of the lore). I find Zelda would make an agreeable or proper choice for Link to be paired with, but I also find that somewhat the flaw. To me, a pairing with Zelda seems more a responsibility, or a "result of". Not to disparage that, but something about Saria seems right to me. That coupling for myself displays a deeper connection outside of circumstance, more of a wild connection of the soul than predetermined fate.  Also, from a more vain perspective, Saria and Link look like they should be together.
If colors could speak it would be Link and Saria.

Link and Malon!  All the way!

From the adorable one-sided flirting Malon does, the little side quest that leads to you being asked if you'll marry her, to everything beyone. It would be absolutely adorable for those two to get together in the end.

My second option would be Link and Ruto. Come on, you get engaged! And The years were good to Ruto, who luckily didn't take her looks from her father. Link is the king that the Zora people need. Come on, who wants to help make Zora's Domain a great nation?...Eh?...Anybody?...Come back guise.