First thing I want to point out here is that I don’t think that Jaehaerys passing over Rhaenys in succession is applauded, at least not from what I’ve seen? What I’ve seen is explanations that offer a more nuanced reasoning beyond Jaehaerys simply being a misogynistic jerk who thought women shouldn’t rule. It might be that Jaehaerys’ decision did derive from a degree of misogyny – Queen Alysanne certainly seemed to think if the Second Quarrel is anything to judge by, but I personally like to think there is a deeper reason because this move shows uncustomary behavior from Jaehaerys. Certainly the guy who made policy changes on the recommendation of his queen and who actively demonstrated political trust in her to where it was said that she ruled the realm as much as he did doesn’t seem likely to pass over his granddaughter simply due to her gender. It also stands to reason that the political partnership of Jaehaerys and Alysanne was likely informed by the crucial political role their mother Alyssa Velaryon and their eldest sister Rhaena played in saving the Targrayen dynasty after Aenys’ weak rule and Maegor’s brutality threatened to do it in, and in winning Jaehaerys his throne in the first place. It is only by the action, bravery and (personal and political) sacrifice of two women that Jaehaerys was coronated in the first place, and Queen Alyssa then held the realm together in the aftermath of war and huge instability for two years till Jaehaerys reached his majority. That the three most prominent women in Jaehaerys’ life were all such active and astute political actors who not only shaped his life but also his reign makes me think there has to be more to his decision to pass over Rhaenys than just prejudice. I also think there could be thematic resonance to Jaehaerys’ decision to bypass his grandaughter’s rights to stave off instability paralleling his sister’s Rhaena’s own decision to bypass her daughters’ rights for a similar reason, and how that juxtaposes against the rampant selfishness of the two sides of the Dance of the Dragons.

Another point of discussion is why concerns about Rhalla and Aerea’s lines only emerged after Aemon’s death and why hadn’t Jaehaerys acted before. That part is a bit hard to discern because we don’t know what Prince Aemon and Jocelyn Baratheon’s fertility history was like. Rhaenys was their only daughter but it is possible that they had either conceived again or at least were trying to since producing a male heir was widely seen as securing the line of succession in a way that a female heir wasn’t. If Aemon and Jocelyn conceived again after Rhaenys or even had children who died in infancy, the issue of the claim of Rhalla and Aerea’s line might not have seemed as dire since there was still hope that Aemon, who was only in his thirties when he died, would have a son, something that was soundly lost with his death. So it might not be necessarily true that concern about his nieces’ lines only came to Jaehaerys’ mind after Aemon’s death as much as that Aemon’s death made Rhaenys’ succession a matter of course which in turn made the possibility of conflicting rival claims to the throne more real prompting Jaehaerys to take action to settle the matter.

As for the Great Council, certainly it is one of the dark ironies of the series that Jaehaerys’ speculated attempt to get ahead of a possible succession debate and war ends up being used to inspire the biggest civil war in Targaryen history. But that’s to blame on Viserys I’s laziness and refusal to deal with the complicated legalities of the succession during his reign rather than on the efficiency of a Great Council. The purpose of a Great Council was to put succession debates to a majority vote rather than the arbitrary choice of the king which is a pretty sound political and legal move all things considered. That’s a solid solution since it decides succession by the will of the vassals over whom the king claimed the right to rule while establishing a body of authority to decide matters of succession allowing for such debates to be settled peacefully and curtailing possible wars. That Viserys I chose to overcomplicate succession by not only ignoring the legal argument that put him in power in the first place when naming his daughter heiress but also by refusing to settle a painfully obvious succession debate in which the two legal precedents clashed is to be blamed on him rather than the Great Council or Jaehaerys I. Viserys set the stage for the Dance by unnecessarily making an already complicated legal matter worse, ignoring the blatant bad blood between the blacks and the greens then stupidly setting the greens up with all the authority they needed to force the issue. Viserys is the one who kicked the problem down a generation while offering no alternate solution and taking no decisive action to settle the matter peacefully. Putting the blame of that on either Jaehaerys or the Great Council exonerates Viserys from much of his ineptitude and willful inaction.