Much has already been said about the various ways that Jaehaerys has neglected, demeaned, and abused his daughters, so I'm going to talk about their marriages (particularly for the younger girls).
Daella and Viserra are both matched off to much older men who already have heirs of their own from a first wife - any children of theirs would inherit nothing. Then there's Saera - Jaehaerys considered all of her teenage companions to be promising matches, except they're really not. They are heirs, but Houses Mooton, Connington, and Beesbury aren't particularly impressive. They're not Lords Paramount (Rodrik Arryn - Daella) and they're not even prominent vassals (Theomore Manderly - Viserra).
So, what gives? Why is Jaehaerys organizing such terrible marriages for his daughters?
My theory: he's intentionally organizing bad matches as a means of limiting the number of half-Targaryens who could one day challenge for the Iron Throne.
The formative experience of his childhood was Maegor usurping the Throne, and one of the challenges of his early reign was Rogar Baratheon attempting a coup to crown his niece Rhaella (who may or may not have been Aerea). Queen Rhaena could have pushed her own claim after Maegor died, and Jaehaerys is lucky that she didn't. Then there's Aerea, an angry teenage girl who was upset about losing her position as heir and upset about being stuck on Dragonstone with her mother, who went and claimed Balerion when left unsupervised. Imagine if she'd successfully commanded Balerion to fly to King's Landing to push her claim - that's not a fight Jaehaerys and Alysanne could have won.
Branches of House Targaryen are a threat. Nieces and nephews and cousins with Targaryen blood are a threat. If preventing that threat means marrying all of his girls off to old men and letting their children inherit nothing, then so be it. Aemon and Baelon are the only ones who really matter.
Jaehaerys wanted to give Alyssa to his heir Aemon, but Alysanne insisted she was "for Baelon," so he accepts this one branch while keeping an eye on them. He ensures his sons are close and sets up Baelon as a future Hand of the King for Aemon. Viserys and Daemon don't receive cradle eggs, and neither one of them claims a dragon (or is allowed to claim, if I were to guess) until after their father Baelon becomes heir apparent. When an eventual succession crisis arrives, Jaehaerys settles the issue clearly and publicly through a Great Council.
As for the other possible branches? Even if all of his younger daughters had married, even if all of them had sons, those sons wouldn't be in any position to challenge the Throne. Maybe a half-Targaryen Lord Arryn would be a threat; a third son of House Arryn wouldn't be, nor would a fourth son of House Manderly. A half-Targaryen Lord Mooton or Connington or Beesbury could never muster an army or gather enough support for his claim. If his daughters have daughters? As evidenced by Aemma, they'll have no better prospects than a Targaryen prince as husband.
His daughters have no value as people who deserve happiness. They're either brides for his sons, tools to be used, or obstacles to be removed.
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