Hmm, on one hand, I see your point about the points of correlation (though I do not think that Rhaegar set Elia aside to go with the parallel to Joffrey and Sansa. That’s a show-only contrivance), but on the other, this is a very unfair comparison. The Targaryen that is truly paralleled with Joffrey is Aerys, not Rhaegar. Murdering a lord paramount in a sham of a trial, escalating the conflict into an outright war with no hope of conciliation, the crown promising leniency in Ned’s case and safe conduct in Rickard’s case only for JoffreyAerys to breach it, taking pleasure in hurting people, hating and deliberately humiliating their Hand (Tyrion for Joffrey, and Tywin for Aerys), sexually assaulting their Hand’s wife, etc. There is a reason Tyrion called Joffrey Aerys the Third in his pov in the books, and that’s because the similarities are numerous. But when it comes to Rhaegar and Joffrey, that’s a different story.

Comparing Rhaegar to Joffrey is extremely harsh imo, whether on a character level or based on how the characters were presented to us. Rhaegar, for all his stupid blunders and the heavy cost they had, did have a valuable purpose: saving the world. That does not absolve or excuse him by any means, neither does it make his actions defensible or acceptable or right, but I will give him the recognition that his intentions were not malicious. He was not acting out of a sense of entitlement that his crown allowed him to do whatever he wanted with no consequence (despite projecting exactly that to the rebels), but out of a misguided belief that magic would ensure that everything turned out alright and he only had to focus on actually making the third head of the dragon. Terribly short-sighted, unbearably dumb, callous and irresponsible his actions may be, but he did not do it to cause harm or pain, neither did he delight in subjugating people or killing them. He simply thought that the ends justified the means, and as long as he was after the worthy end of saving humanity, it was worth whatever measures he took to ensure it. In that, he is not at all different from Melisandre or Bloodraven, all three aspiring to a higher purpose and showing willingness to do whatever it took to get there on the belief that the goal makes their questionable means worth it, and that the coming fight would exonerate them.

That is in no way comparable to Joffrey who did think that his crown gave him the green light to do what he wanted and who internalized the Lannister ideology of fear and violence, which was not made any better by having an abusive father who gloried in violence. Joffrey had no higher purpose, no real motivation but to assert his power and feel kingly and strong. He was a sadist who found pleasure in subjugating people and causing pain, and who saw people below him as insignificant livestock. Joffrey routinely dehumanized people and found it empowering and satisfying to do so. He showed a degree of cruelty and of delighting in others’ pain that is simply not there in Rhaegar who, despite his many blunders and the toll they had, seems to have been a relatively decent person, albeit a dreamer willing to cross the line ~for the greater good~. But at least Rhaegar, unlike Joffrey, did have a greater good he was pursuing.

Rhaegar and Joffrey were also introduced to us in vastly different ways in the text. Joffrey was the handsome prince Sansa fell for pretty much immediately, the excellent match that was only belied by Lysa’s accusation that the Lannisters murdered Jon Arryn, but we got warning signs that this was not the case immediately afterwards, starting from Joffrey’s arrogant superiority with Robb in the training yard to his reaction to Bran’s fall to the incident with Mycah at Darry. From the moment Joffrey interrupted Arya and Mycah, none of us were under any illusion as to what that kid was, and he only got steadily worse from there. So while Joffrey was that handsome charming figure for a hot second, he quickly showed his true colors not even half-way through the first book, and continued to grow nastier as the books progressed. But the main thing about Joffrey’s story wasn’t about how the readership viewed him or even about breaking us from the opinion we formed about him – the truth about Joffrey came far too quickly and was alluded to before that for this to be the case – that was more about breaking Sansa from the illusion she built about Joffrey and what he was, not the readership.

But it is about the readership with Rhaegar. He was not introduced as a remotely nice figure, but as a violent rapist who carried off Lyanna out of personal pleasure and incited a war that cost Ned nearly his entire family.

But as the story progressed,

Robert emerged as an unreliable narrator

and a hypocrite with a tendency to romanticize and alter narratives to fit his
view, and Ned’s lack of animosity towards Rhaegar was noted, which was a pretty clear neon sign for us not to take Robert’s
story at face value, which some took as evidence that the true story is
the total reverse of what Robert said it was, and that perhaps Jorah and Dany’s account of the noble Rhaegar was much closer to the truth, despite both Jorah and Dany being even more of unreliable narrators than Robert.

But of course, Jorah’s and Dany’s truth –
later supported by Barristan Selmy – was that Rhaegar loved Lyanna and
died for her, which falls right in line with courtly love conception of
romanticism that tends to absolve the characters on the grounds of love
being so pure that it makes up for everything else.

Also, note that the one person who disparaged Rhaegar died in book one, and
since then we’ve had nothing but people who romanticize Rhaegar and are
invested in the idea that he did no wrong, or that if he did, it was out
of love and love forgives all. For multiple books, the
narrative only tells us that Rhaegar died for the woman he loved, and that “Prince Rhaegar loved his Lady Lyanna”,
and other similar sentiments. Rhaegar crowning Lyanna at Harrenhal
(something straight out of a chivalric romance), taking her away from an
unwanted marriage, and dying on the Trident with her name supposedly on
his lips paints a rather romantic picture. Even the imagery used by the
narrative is romantic:
“rubies flew like drops of blood from the chest of a dying prince, and
he sank to his knees in the water and with his last breath murmured a
woman’s name”. It’s all terribly tragic and terribly romantic. It’s not
hard to see why many people believe in that version of the story, had
come to expect it even, and have come to analyze Rhaegar’s action
through that lens, even though it still does not change the power
imbalance in the story, or the glaring consent issues, or Rhaegar’s
political stupidity. So Rhaegar’s image actually started as very bad and steadily got more and more romanticized as various characters added to the description of the chivalric prince. It’s only when you look closer and beyond the usual romantic tropes that the glaring flaws in that narrative emerge, and you notice that the actuality of Rhaegar’s actions, even if they were solely out of love which I highly doubt, are disturbing.

That does not mean that there is not an in-universe disillusionment coming, but I’m not sure how much it would revolve around Rhaegar. Dany is going to have to face the truth about her family and the rebellion at one point, but how much that pertains to Rhaegar’s image in her eyes, I don’t know. For better or for worse, and no matter what Rhaegar’s motivations were, the fact remains that Dany already knows that he insulted Elia publicly and that he made off with the intended of another lord paramount. Believing it was out of love gives this story a noble veneer in Dany’s eyes, but so would the revelation that Rhaegar was trying to save the world, which makes me wonder whether Dany would fully grasp the ramifications of Rhaegar’s actions, especially with her romanticizing tendencies (though who knows what will happen when Jon discovers his horrific origin story and how that reverberates through whatever relationship he has with Dany at the time) But I fully believe that Dany’s disillusionment would be mainly about the collapse of the image Viserys sold her of Aerys and the nature of the rebellion, to parallel Sansa’s own revelation about Joffrey and who the Lannisters truly are.

Whether Dany’s revelations would solely be about Aerys, though, with the part about Rhaegar being kept for Jon’s own story remains to be seen. Hell, whether GRRM would actually address the consent issues in the story of Rhaegar and Lyanna remains to be seen. I do have my fears tbh because his track record in dealing with consent is not exactly the best, and he has been known to play his tropes straight.