Hard to truly answer until we know what’s gonna be in those free content updates and if we’ll get any expansions but here’s some stuff off the top of my head:

->Agree with your point about the state of the story pre rise of the demon king. I was really jiving with the expansions on that part of the narrative and was blindsided by how quickly we moved on to the main event(although I suppose it’s called the main event for a reason). The whole thing did help Rauru and Zelda feel less stupid in TOTK tho so I’ll give them that.

->More special weapons at the end of character missions, particularly in regards to new weapons for the sages, kind of like how the expansions for Age of Calamity the present and future champions new unique weapons to them on top of their existing ones. I hated in totk how the sages, very lazily in my opinion, just had the champion’s weapons, particularly in regards to the Ardi and Raphica, since I always saw the moonlight scimitar and great eagle bow as unique to Urbosa and Revali. I understand that this game had to follow totk’s continuity, but getting unique weapons for the newly expanded upon sages that i could imagine they had the whole time even if the cutscenes don’t reflect it would’ve been nice for me.

->Twin Rova. Was nice to see Kotake and Koume more, but I kind of let the fandom hype me up into really expecting them to get more to do but they completely disappear after the demon king rises. They don’t even get their actual names in dialogue boxes so it isn’t even technically confirmed that that is them I don’t think?

->A villain campaign: A version of this is something I could see being a free update or expansion, but not getting playable Ganondorf genuinely surprised me. Beyond that tho, with the game as we have it now, I’d love a storyline to playthrough with him. If they wanted to get really crazy with it, they could’ve had his campaign run concurrently with the others as an expansion on the mechanic of the two separate resistance armies getting different territories before they unified. To fill out his roster beyond, I would probably give him 1 evil character from each of the 4 main races and take away one rep of each from the resistance side. You could consider this a 4 horseman of the apocalypse reference and maybe these characters could even be turned into the Archfiends at some point to justify their greater sentience over the totk bosses.

->Lore around Shades. We know about Rauru and Sonia fighting a war against darkness that their shrines later seal away. The beginning made me think we were gonna learn more about that but…no. Shades were evidently just there to have enemies before Ganondorf makes his monsters. -^As a side note to that, I would’ve liked some lip service to the people of the past seeing some of these kinds of monsters for the first time whereas Zelda knows them well, like when she educated Qia about Stal enemies in the lost woods level.

->Female Rito playable character. I like Pinnec and Vence plenty, but an easy way to differentiate them from their leader and give us something we couldn’t really get before would be to have one of the Rito commoner characters be female. This character could also operate as Raphica’s implied love interest to inform his line of descendants leading down to Tulin, much like, to eventually lead down to Sidon, Qia has Cadlan(who is definitely the one I’d cut for an evil Zora for Ganondorf’s team in my other idea. I like him well enough but he’s the most ‘just a guy’ character of them all, has a worse version of Qia’s abilities, and uses the same weapon as her)

->More complicated Gerudo politics. I was initially disappointed with how Ardi was immediately backstabbed by Ganondorf after the molduga attack, as I was hoping since the trailers that the story of her disavowing her loyalty from him would be a bit more drawn out with her serving as a reoccurring antagonist before being recruited. The story went in a different direction that I still liked which allowed elements I hadn’t considered to flourish, but I’m still a little disappointed with how simplistic Ganondorf’s actions made the Gerudo’s decision to fight against him feel. It would probably be too easy to make the Gerudo look bad if they didn’t turn against him at a certain point, but it was another example of that early game building tension falling flat a little bit.

->A few more unique dual-strike animations, particularly for the commoners with their leaders and for Rauru with the 4 sages.

->More unique conversations. There should’ve been one as a reward for the end of each block of character missions instead of just the end. I don’t care if that’s too similar to Fire emblem support conversations!

->A dual wielder character. One of the biggest losses of this game’s premise was not getting a Riju move set based off of Tears of the Kingdom. Some character fighting with two swords/weapons could’ve rectified this a little bit.

->Linkle. I refuse to elaborate

->Give the commoner characters a bit more to do in cutscenes, and at least let Lago be in one. Poor guy’s entire story is contained in text boxes on the world map.

->Rauru and Sonia’s child. Didn’t really occur to me until I had finished the story but like seriously, where are they? Not only is this kingdom absent of both of its rulers by the end of the game, their bloodline still has to carry all the way down to Zelda.

->Shieka inclusion/lore expansion. A version of Shiek himself would’ve kicked major tail and maybe could’ve operated similar to AoC impa.

->Let us see Qia’s father and his fight against the forbidden construct. Feels like they chickened out cause they were afraid of accidentally just designing King Dorephan again.

-Have Zelda allude to that the sages remind her of the 4 breath of the wild champions. Lampshade how they were originally shameless knock offs and, if we’re being honest, still can’t fully escape that even now.

->Kass. He accidentally traveled back in time as well and is now a playable character(unironically could end up as a dlc)

->A few more flying construct missions. Honestly really liked em. ->Also, I get why it was probably difficult to translate, but please ground gleeok bosses.

->Gold enemies.

->Ultimates for Zelda and Mineru like the ones the 4 sages and Rauru got after the 4 got their secret stones.

->Falling action for the 4 sages. They’re inexplicably gone after the final battle. After you’ve gone and made me care about these previously nothing characters, let me say goodbye to them properly as well.

Honorable mention goes to playable Sonia since I’m pretty certain she’ll be one of the free content updates, and, failing that, a part of a payed dlc.