Okay first off I don't think Link and Zelda are romantic in every reiteration. I just need that disclaimer
I tried to associate the species with people's elemental powers or their narrative spots in the stories
For the sake of I like drawing mixed species all gerudo do have dominantly gerudo traits but there will be some random bits of whatever else is mixed in but the other traits don't usually pass down
Garmadon is half Gerudo half zonai
Misako is the second hylian princess, her sister is name Zelda as she was the first daughter but Misako is actually the zelda reincarnation but that won't be discovered for a while
Lloyd is Link reincarnation and he is hylian, gerudo, and zonai
Kai and Nya are Zora and shekiah but they are descendants of cobbles
Zane is a construct powered by a wizzrobe staff (this currently makes the most sense but if I figure out something better I will update it)
Mystake is a gerudo and sheikah her shekiah traits do not pass to garmadon
The overlord is the malevolent spirit of Ganondorf
The serpentine will be kept the same but instead are imprisoned in the depths but they used to be dotted all around
Mystake pairs up with FSM who is one of the last zonai neither desire a long term commitment
She gives birth to Garmadon who is a male gerudo and fears the worst and brings him to his father
Fsm has started to settle down with a hylian woman who is happy to adopt Garmadon as her own
Mystake goes back to gerudo town and Garmadon stays with fsm and Wu's future mother
Wu is born and they are raised as equal siblings but most townfolks shy away from garmadon, he knows he is treated differently but doesn't understand why
Garmadon and Wu train as warriors under their father and are taught zonai traditions
There is some sort of competition that allows the brothers to meet the royal family
The serpentine (currently scattered around the land) are getting into skirmishes with expanding villages as they're tribes are expanding as well
The tribes start to gather and unite against the other peoples of hyrule/ninjago
The gerudo discover Garmadon and are very displeased and it causes issues when fighting battles
Garmadon has the idea to imprison the serpentine in parts of the depths. He makes the plans and delegates and leads which causes the gerudo to recognize his leadership skills and more open to the idea of his existence
His idea winning the war also has caused the hylian king to offer him any boon he desires
He asks for Misako's hand in marriage
The king laughs and declares only a king may marry either of his daughters
The gerudos garmadon fought with argue that he is destined to be their king and therefore he should be allowed the princess's hand
The king relents but says the marriage will not take place until after the coronation
Garmadon is crowned and the former chief is not pleased and is even angrier that he is not even marrying another gerudo but is instead marrying some hylian
Misako encourages archeology while she specializes in anything regarding prophecies 
Shock across the nations at another male gerudo, disgruntlement about gerudo traits not really passing down to him
And that would be the first story in the au might do an epilogue about Lloyd finding the master sword but that would be in the next one, I just need to flesh that one out more