Baratheon as a name is only 300 years old. Before that the family was House Durrandon (and I'd laugh at anyone who says there's more of Orys in that bloodline than Argella). Nobody seemed to object when Orys decided to use his own family name instead of adopting his wife's (despite the fact that the name Baratheon for all we know is something he pulled entirely out of his ass). Nobody objected to Daemon Blackfyre or Jacaerys Velaryon because they didn't use the last name Targaryen; everybody knew exactly what they were. At least Stormcrown means something, with its ties to Arlan and what Jon is.
No need for the name Baratheon to die anyway. Edric Storm (our newest little brother) is being legitimized as well. With Renly being notoriously disinterested in women (and unlikely to rebel against us, please remember that in canon it was Loras who drove him to rebel not out of personal ambition but because they wanted Margaery to be queen) I don't see him fathering an heir, meaning our little brother (who I very much would like to take as our next squire inb4 Edric DP sink) can be our heir to Storm's End. Marry him to Arya (he's only 2 years older than her) and we've simulataneously made all of Westeros' dragon riders part of the royal family, given Robert his him/Lyanna match that he wanted in canon, and set things up to marry out future firstborn to a grandchild of Robert Baratheon (not fully necessary but I'm sentimental and actually would like for future Stormcrowns to have the blood of our adopted father, the Storm King).
I agree with people who have suggested reforming the kingdoms a tiny bit, because putting Harrenhal into the Crownlands (with some other lands to avoid ugly borders) will reduce the Riverlands. Giving the Golden Tooth to the Riverlands (the heiress Alysanne Lefford is unmarried in canon and can be wed to some second son of a Riverlord) will not only make up for it with land and income but also give them a strong natural border (something that they've always sorely needed). If we were actually a Baratheon I would even suggest making our heir Prince of Storm's End like the Prince of Dragonstone, but instead I'm fine with Edric's line one day setting up in there (optimistically). The Brax lands also would fit into the Riverlands, as some people suggested in rolz.
What to do with House Lannister really depends on how they move after this. I don't dislike some of its members but they are our enemies now and we do need to be careful. I had the semi joking suggestion of, if they rebel, marrying Rickon to Kevan's young daughter Janei Lannister and making him Lord Paramount of a reduced Westerlands. Some people seemed to like it though it's a bit tinfoil, and I like the idea of Jon being inspired by chessmaster Robert and ending up with five Lords Paramount as his "brothers" (Robb, Bran, Rickon, Willas, Edric). Rickard Stark's ghost would pee his pants.
I like that there's discussion about what to do with Maester Tuck. Personally I think after getting the news that Ned Stark is dead Jon will be in a pretty bad mindset, but I advocate interrogating Tucker for everything he knows before doing anything. I acknowledge that he could have killed us and could have told about Arya's dragon, which are excellent reasons to hear him out before doing anything, but I'm also furious at him. We'll see how the update goes and then vote at the time.
The Crimson Sept as far as I know stole the dragonglass as a "just in case" measure. They've sold most of it for a profit and only kept a small amount. It doesn't really matter to me that they planned to use it, because as I've speculated before, I believe the religious fanatics would only move against the Others once they got south of the Neck and had already killed all the northern heathens (unless we hypothetically convinced them otherwise) and that any obsidian weapons will be of infinite more use on the Wall or at least against the Others before they raise too great an army to defeat.
With Jon's new position as both crown prince and enemy of the Lannisters, I actually think we should get married as soon as possible. Not only do we need to father heirs (something I'd like to see in the quest if only to see how Droman writes Jon as a father) but it will also better secure our alliance with the Reach. Healing Willas is a high priority as well, as is speculating about good spouses for our new goodbrother and goodcousins. Personally I think that with their strong ties to the new prince, House Rosby could reach high enough to marry Willas Tyrell or Horas/Hobber Redwyne. Walder Frey would be... mixed on that considering his name is also going to die and be replaced by mountain savages.
I anticipate some sort of response from Tywin definitely, but first I want to see the end of the year omakes (so excited for some people's reactions) and if Tommen and Myrcella are successfully arrested or if Lannisters/Littlefinger interferes (though he may be busy planning to woo Catelyn). If an assassin is sent I strongly believe that we'll be given an opportunity to see it coming and fight back. If not it be both ridiculously unfair and impartial.
I do want to repeat that I really dislike the idea that Willas would turn on the rest of the realm and his goodbrother (or former goodbrother as some of them seem to hope) because he loves Oberyn so much. Not only is that portraying Willas as too unintelligent/uncaring to acknowledge that Oberyn is using him, but it makes him seem even dumber by risking dragonfire on his armies just for a few romps in the hay with someone who is far more attached to Indira Varma anyway. Why wouldn't he be friends with Jon, who he would call brother and who would have healed his leg (we're hopefully doing that soon). If he tried anything that stupid I would fully advocate cleaning him from the gene pool and making the superior Garlan our LP of the Reach (and if he joined the Rebellion then Highgarden could go to a second son by Margaery, sigil a blue rose because I'm a sentimental bitch).
Aegon will come, of that I'm pretty sure. He has the Golden Company (10,000 men) and Dorne (pretty shit offensively but maybe ~20,000 men. Most of the Seven Kingdoms could challenge him without the unity that I think Jon Stormcrown will inspire, which leads me to believe that there will be other threats surfacing at the same time. My best guess is it will be a combination of Others/Wildling shenanigans and the Lannisters making some sort of move. Considering that the last we heard of Viserys (if I recall correctly) was that Volantis was being attacked by Dothraki, what happens if Aegon comes to his rescue with the Golden Company? Remember his dragons are still young and too small to fight well. Aegon could demand some price of Viserys: the hand of his sister Daenerys, one of his dragons, his support against Robert Baratheon, or hell, he could demand all three. Worth thinking about.
Would be funny if we could avoid a war by using Oberyn's favor to arrange a peace talk and promising an exchange of marriages (Aegon and Arianne rule Dorne, their firstborn children wed ours).
I think I've covered everything intelligent/interesting being discussed in the pages that accumulated while I slept. Good discussion topics. Love this quest.