Just saw all the discourse on the parents love triangle lol. Tbh I never did put much thought on it in the first read but holy cow you really thought all of it through. This is such a complex triangle. Can’t wait to see the prequel when its out. I do have a question if you dont mind me asking and no need to answer if its too spoilery but as I started re-reading I remember in the story it said Rheagar did not join Lyanna’s bed for 2 years after the rebellion. Did he only sleep with Elia during that time or was he focusing on making amends with Elia? I guess I got curious if Rhaegar and Elia ever took bed/intimacy like husband and wife after everything or if it remained just platonic.
Honestly it kinda got out of hand, as it often happens.
I don't usually plan ahead everything I write, which is why at times I write myself in a corner... anyway I have a general idea of where I am going and what I want to achieve but plots kind of just take a life of their own and as I kept on writing... and around the time I posted the chapter in which Jon recalls Rhaegar speaking about Elia's kindness I kinda knew I wanted to write a prequel about Elia/Rhaegar/Lyanna triangle.
Elia is far gentler than any of us deserves , his father had said. Aye, Jon wanted to reply, but that kindness cuts as sharp as a knife , he thought watching his mother’ pale face and the king's haunted gaze. A man ever torn between duty, respect for a wife who was far kinder than he deserved — Jon could admit now — and the blinding love that bound him to Jon’s mother. - chapter 13, TotBKu
Which again, goes a long way to show us how biased the POVs are. Is it as Jon thunks only duty and respect that bind Rhaegar and Elia?
Now, onto your question. It is a bit spoilerish but I may try to reply at the best of my ability without spoilering too much. There are several reasons for their initial separation.
A) Jon's birth was taxing and Lyanna was a teenage girl. She almost died and would have actually died if Ned had not been there, as she tells us herself.
Her own pregnancy with Jon had been difficult and Ned’s presence had literally saved her life and that of her son. - Chapter 16, TotBK
B) Once Ned got her back from the Tower of Joy, Rhaegar impeded her to return home even though he would not keep on to their marriage, as he had set her aside to appease both the Faith and the Martells. I will not go into the details about how he achieved that, but it is safe to assume that that coupled with the whole bastardising Jon' matter would be played an important role too.
C) Rhaegar was playing nice with both the Faith and the Martells. Whilst we are told that he married Lyanna in some capacity, he set her and her son aside, and was forced to make amends with the dornish and the Faith and the Realm whole. The Realm could not blame the king who had won the Iron throne so the blame would befall Lyanna and Jon some way as Rhaenys tells us.
It had taken them years before they had settled and understood her mother was not someone one could easily deliver himself of. The faith had never conceded Rhaegar the annulment he had pressed for when he had taken Lyanna to his bed. He wanted to make her son legitimate too and he could do that only if he was born trueborn, as any other acts of his parts would be tantamount to insult to the dornish, and a reason for war. - chapter 8, TotBK
Which also explains why Rhaegar had to maneuver for years before he could safely issue a decree not against the first one he issued (that Elia was his queen consort and his children by her trueborn and heirs to the crown) but in addition to it, which also explains the move to add the implication of an election by the lords of the fittest son to inherit after him. He was being a bitch, basically.
D) Lyanna's own character. She's stubborn and at the time she was a teenage girl who risked everything, lost her father and her brother, lost the respect of her people and her homeland to be with her prince and be married to him only to be set aside and see her son bastardised... the son that, if he had gotten his annullment would have been de facto the heir apparent to the Iron throne. She lost everything and gained nothing so she was understandably furious about it.
Also, I think I can give you this little peek into the prequel without it being too spoilerish.
"I command you not to...It is forbidden," he said voice of steel and eyes of feather "I forbid you to die", yet the queen could hear in his voice the tremble of the boy she had first met in the Water Gardens. He had been drenched to the bone, and she still recalled how her hands trembled as she offered him the towel to dry his silver gold tresses. He had steadied her and had called her 'my princess'.
She stared at him for a long moment, reminded of that boy, then sighed "Come here, husband" she said and urged him closer, offering him her hand, "this is out of our hands, and even you cannot command the Gods' will if to their side they choose to call me."
So, in a certain way, they did make amends. And as Rhaenys said, her mother chose to love Rhaegar and kept loving him despite his flaws and his best attempts to drive her away from him.
So yes, it's going to be raw and feelings and emotions packed for sure.
I do hope you enjoyed the reply! Perhaps I will post a few snippets here and there about the prequel, but since the first chapter is set almost end way through the second installment of the main duology I fear we will have much yet to wait, sadly.