It's badly done, but here's globally the links and Zelda who are related (genealogic tree)
I'm gonna do another one because it's kinda confusing
Alsooo I'm so sad I got 2 theories/ship for that that can't be merged together T^T because I like Raven x Sheik, but I also like theory of oot Link and Zelda being related... :(( so rip the second theory... TvT
Rambling under the cut
So, yeah, Ballad and Aviator are together (and Goose but I forgot to add him lmao), and they started the goddess' bloodline.
Mini is their ancestor, but I have no idea who she could marry, because Mice is aroace, so her husband/wife is a ??? For now, but if you have any idea who it could be, I'd take! Same for every ??? Too.
In the childhood timeline, Light is Sheik's descendant, and she's the ancestor of Ribbon.
In the adult timeline, Tetra's also Sheik's descendant, and she and Waves are Guardian's ancestors. Guardian is in a relationship with Smoke.
Woods and Malon are Wolf's ancestors.
In the downfall timeline, Raven and Sheik have kids (yeaaah they're both guys but dw it's magic), and after some generations pass, Melody and Sage are born. They're siblings, but don't know it at all until the end of alttp. (Link thought of that possibility when his uncle told him "save Zelda... She's your... Argh I'm dead" thing)
I actually don't know if I want Marin to return or not, so I put ??? On who he's gonna have Ring with, but probably Ganthi I think? Because Marin's not dead in my AU but in Waves' timeline, so I could technically bring her back to Melody, but I also like my tragic doomed ship with a bad end...
Anyway, Ring is born, and he knows Maiden's his cousin, but never actually met her until the beginning of the manga/game. He also met Raven.
Maiden continues the goddess' bloodline with Sun, and then finally Rift, who's totally onto Donna.
Void somehow just popped up like that lmao
For Tears and Dragon, it's a bit more complicated...
Actually, the queen of Hyrule had a relationship with a royal knight, without the king knowing. She got Tears with the knight 1 years before having Dragon with Roam. When the king acknowledged her other relationship, she had a trial, and was sentenced to death for infidelity to the king.
Tears and Dragon never knew they were siblings, but Mipha somehow figured it out.