N + C = J
Joffrey was poisoned by EVERYONE at the wedding except Cersei, Sansa and Tyrion.
Ned Stark lives as a pigeon in KL
Craster's daughters weren't actually his daughters, he was just getting cucked every time.
fAegon = Rhaegar + Cersei
As we know, House Tarth has a connection to the Targs for some reason, and Dunk.
Many people think this is because Dunk knocked up Rhae or Daella and they were married off to the Evenstar, where one of them had Dunk's child, and passed it off as a Targ.
I propose this is through Maegor Brightflame.
This is the timeline.
Dunk goes to Tarth and knocks up a Tarth heiress with a daughter. This SHOULD parallel Bael the Bard, a lowborn who gets with a heir. She is quickly married off to some landless second son who is OLD, and they have Dunk's child.
Enter Maegor Brightflame, who is VERY dangerous as a potential threat to Egg's power. Dunk proposes sending him to Tarth to marry the Tarth heiress, as although Tarth is rich, they aren't exactly the most powerful, and Dunk's hook up buddy is the ruling Lady, so can keep Maegor in check.
They have a child, Selwyn Tarth who COINCIDENTALLY is the perfect age for Brienne's father, being born in around 255 AC, and Brienne being born later in 280 AC.
This lines up with everything we know about Brienne's parentage, and means that Maegor is suppressed. Its even possible Selwyn isn't told about who his dad actually is, which means that line of the Targaryens is gone as a threat.
Keeping the Freys around was silly, when removing them was easy enough, and everyone would support it.
They marry into them because they are powerful. If they were attacked, no one would lift a finger to help the Freys out.
Its explicitly mentioned in Feast that the Freys and the Red Wedding was one of the main reasons why the Sparrows gained so much traction. In any religion the Freys were cursed by the gods for breaking guestright, something EVERYONE takes seriously. Killing them off keeps the FOT7 on your side.
Walder would obviously try to send proof to the realm Roose and the Lannisters were involved, but who would believe him? The Lannisters could easily say that Walder did it of his own accord to try to gain favours from Kings Landing, and that he would gain as a result.
House Frey as a result of the end of the books got various marriages and castles as a reward for the Red Wedding.
They got Daven to marry a Frey.
They got Lancel to marry a Frey and claim Darry through her.
They got Emmon's brood to claim Riverrun (partially because Genna was his bride however)
And they will definitely be around to claim Rosby through Perwyn or Olyvar.
No one likes the Freys as a result, and it would be easy, and politically convenient to dispose of them, giving Lord Baelish a far more secure hold of the Riverlands, given many a major vassal is gone.
Tywin getting rid of the Freys would solve a LOT of problems, and gifting it to another house would ensure loyalty.