DoS2 is amazing, but one of my main gripes is that there are points in the story where it feels like I could have had more input on a situation or a line of dialouge seems out of place.
Examples: When you give the swornbreaker to Sadha she says "you never cease to amaze" though this is confusing because it implies that she has been spying on you somehow, but the player is unable to persue such a query.
You can't ask the elves who saved Saheila about the fates of Fort Joy's other prisoners when speaking to them.
The player is unable to ask Lucian on how he intends to survive being purged or do it to him before sacrificing yourself in the Ultimate Sacrifice ending.
The Mystic tag on a lizard character has dialouge that implies a history with the house of dreams, yet this conflicts with dialouge in the Red Prince questline.
Necromany is seen as evil yet you can buy skill books of the practice at the town market.
Your companions never bother to ask your name, both for origin characters and base names for custom ones, not even in the epilogue.
Certain lines of dialouge repeat when you speak to an NPC with a another character although your entire party is present.
You can never tell Barhamos to show respect to another Godwoken who risked their hide keeping prophecy boy alive.
And none of the information you give to Cranly Hewbert has an impact on Rivelon's future.
I know I might be mistaken on some of these and that Roleplay ability ect. Are huge factors that make some issues unchangeable, but I do believe that there are some things that need rectifying. Whether you guys do it in a remaster ,the next giftbag or at all isn't up to me. But I still hope that this information can make future games even better.
Just sharing some thoughts based on your points.
Regarding Sadha, I don't know if it's just that she's been specifically spying on you. I just take it as the more general that she's heard of your actions and/or reputation. There are a few characters I remember meeting for the first time who upon meeting mention that they've heard of your character or their exploits. I just take it of word of your deeds traveling around.
For Saheila and the elves, I get the impression that the game doesn't assume you care about the people at Fort Joy, particularly since after obtaining the the Lady Vengeance you're not given the opportunity to invite any of the prisoners to come with you even after all the magisters are dead. This really sticks out with that elf you meet early on who had been waiting for that magister lizard to return so that she could take her and her adopted human daughter to the sanctuary where they would await a boat to get off the island. Despite you completing everything that the magister lizard was going to do anyway, you can't invite that elf along. So I guess the game makes the assumption that you don't care about the people back on the island since you didn't try to rescue any of them yourself.
For Necromancy, I think the most evil part of it is raising people from the dead and using them as slaves. With the Necromancy skills that you use, none of them really involve doing that. Bone Widow isn't really raising someone from the dead but instead is more like creating a golem using bones. And Raise Bloated Corpse looks more like a monster that is spawned from bodies rather than actually raising that person. If I recall, the companion dialogue that occurs when you obtain the soul jars of those necromancers in Braccus Rex's vault implies that the the disgust over their actions is using the dead as slaves primarily. But that's just what I think.
As for names, I think it's just one of those things we have to assume happens during unseen dialogue. If I recall, I'm not even sure if Sebille gives you her name when you first meet. But I don't think it's that unusual, since when you first meet the origin characters you're not necessarily friends, but just people working together to escape Fort Joy and Reaper's Eye. Initially, there isn't even the promise that you'll stick together once making it back to the mainland, so perhaps names were not important. Besides, only a small part of dialogue is shown while on the road together outside of specific situations, usually the responses that companions have as a reaction to certain events (when the yellow exclamation points appear above their heads). But similar to going to the bathroom, I like to assume there's more dialogue happening along the road as they travel together. As an example, I remember having Ifan as a companion, and one of the companion dialogues with him when you chat with him has him talking about the memory of some thing that happened with you and him that I didn't recall ever actually being shown to have happened.
The repeating lines I think is just to take multiplayer into account, so that if player one speaks to an NPC, player two can still speak to the NPC and get the same information.