The problem with that is Tywin is Tywin - he is demonstratively literally the worst ally to have. He actually actively plans to supplant the Boltons immediately upon eliminating Robb Stark, and the Lannisters are now actively planning to throw the Freys to the Riverlords. Actually, it is even worse for the Boltons - the Northerners could have literally flayed all of the Boltons before word even reaches Kingslanding that there was trouble. Maybe this is just me, but it just seems incredibly short sighted. And furthermore, Roose Bolton should be aware of the deep seated cultural reverence for the Starks. The idea that the Boltons could replace the beloved Starks is...odd, considering the reactions of the Northerns post Red Wedding - even the "only Northmen for the last 1000 years Manderlys" literally shout their defiance "We swore that we would be their men. Stark men!" Maybe it is purely plot convenience, but it appears like a monumental blindspot for someone like Roose Bolton to have.
While I agree with everything you said about Tywin, the Northerners couldn't just kill the Boltons like that, because the RW tore the North apart. Even with Tywin dead, plenty of Northern lords were held in Frey/Bolton captivity, and their levies either slaughtered or scattered. Roose still had almost all of his men, alongside Frey men, who had also remained mostly untouched by the war. Even with Tywin not doing anything ( and even if, unknowingly to Roose, plotting to put a Sansa/Tyrion child in WF); if he were alive, Stannis dead, and Dragonstone and Storms End were in the Crown's hands, the idea of openly rebelling against Roose would have been unthinkable.
However, with Tywin and Joffrey dead, a child on the throne (and his legitimacy being called into question), and Stannis alive and well with a large army in the North, the Northern Lords are in a much more opportunistic situation. If it weren't for these factors, the North would be a much more stable, albeit ruined and spiteful, part of the realm.
Also, with winter arriving, I doubt anyone not as desperate as Stannis would even think to besiege the Dreadfort, let alone Winterfell.
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