If Lyonel's daughter marriaged into the Estermonts it would clear up the confusion of the familial relations.https://www.reddit.com/r/asoiaf/comment ... gests_who/
Someone did a markedly better write up of it with the above link. (More likely it was just a mistake, if it wasn't the Estermonts by right inherit, being the last descendents of Lyonel Baratheon.)
Then after that it goes into murky semi-canon waters with the Blood of Dragons MUSH. Which is fortunately backed up by the aWoIaF book and dangerous women.
One of Borros Baratheon's daughters married into House Blackwood (Husband of Bloody Ben). This I'd take as damn close to canon considering Borros' four daughters are discussed in the Dance. While one of them was betrothed to Aemond.
Now following simply semi-canon, Arion Baratheon's (Lyonel's grandfather) sister Lyria is betrothed to the Crakehall's. While around that time (before third son Gowen and Tya Lannister) a Baratheon maid married into the Lannisters. (The Mod has it as one of Arion's daughters, an aunt of Lyonel.).
Anyway, if they're all taken together. We have;
House Tully (cadet branch,Brynden Tully. Brother of Kermit Tully married Sarya Baratheon, daughter of Corwen Baratheon)
House Lannister (cadet branch. Can't be the main line despite what reddit cooked up with Elayna and Mathin Lannister, he'd have to kill his nephew Damon, Gerold's father to take Casterly rock. I'm sure the Mod has it as Symond, Damon's brother. Agewise Mathin and Elayna would fit. Just as how Symond and Arion's daughter fits.)
House Crakehall (Youngest daughter of Corwen Baratheon. Betrothed/married to Garen Crakehall.)
House Rowen (daughter of Borros married Thaddeus Rowen)
House Targaryen (via House Blackwood and the marriage of Aegon V and Betha Blackwood) attainted by Baratheon's.
House Stark (via House Blackwood and the marriage of Willam and Melantha)
House Waynwood (this and below, the daughters of Jocelyn Stark)
House Swann (through Ser Orys, a uncle of Lord Corwen Baratheon)
House Waxley (through Lady Maelane, aunt of Lord Corwen Baratheon)
House Velaryon (via Jocelyn Baratheon's granddaughter Baela Targaryen, great granddaughter of Boremund Baratheon. who married Alyn Velaryon)
House Hightower (via Rhaena Targaryen, as per above, if the eldest married back into the Hightwoer main line, which I highly believe they did. Married Garmund Hightower.)
House Penrose (via a daughter of the Hightower match, which would fit with the Penrose's being Targaryen cousins as Elaena's line is discounted.)
- Four other Houses from the Hightower daughters.
Basically it'd be a clusterfuck.
After that just throw the Wensington's and Bolling's in. The Bolling are canonically Durrandon cadets, it's unknown in regards to the Wensington's. I'd hope personally that would be Sarmion the Stormbreaker who starts that cadet, as his nickname is cool.
If we have no Baratheon's left at the end of the books, I'd hazard a guess that Edric Storm made legit and married to an Estermont or Swann would be the most likely to cement rule in the Stormlands.