3) The dead tree and poor druid in Act 3
(can you tell I like druids?)
7) There are a couple of refugees with lines that beg you for money, but you can't give them anything.
I similarly encountered people in the city who I wished I could interact with. There's a tiefling child with murdered parents, and I instantly cast speak with dead on them to nothing. I similarly wished I could have helped the druid with the tree. If I'm being reasonable it's probably true that these were always meant to just be flavor text, as creating even small quests for all those citizens would be a huge amount of work.
5) Unless you are a lore junkie, you don't really know the strange ox is evil. He's a great ally, but why does risk his life for the simple favor you do him? Does he have a connection to the city? Does he really want to retire? Or does he have some ulterior motive to getting inside?
I was confused on that. I did an evil embrace the urge run and my murderous durge called him pathetic for turning his back on the slaughter. He refused to change into his monstrous form and died in cutscene as I hacked him to bits. He literally said that he didn't want to murder, he just wanted to be an ox.
Everyone talking about Omeluum-
I love Omeluum and it definitely makes sense that he would also fight in the final battle, though perhaps as a 'weaker' option since he doesn't seem like the fighting type. I would also settle for him being some sort of ally summon. I think the rationale the game has is that he's not present at the moment the decision about what to do with Orpheus, and therefore can't be called in to help.
Along those lines, I also wish you could volunteer
any party member to become a mindflayer, maybe with a persuasion check (or having convinced them to tadpole themselves earlier). I know Karlach can become one but don't know about anyone else. Either way, it would be fascinating to see who could do it. Wyll, Gale, and Shar's Chosen Shadowheart all seem like prime candidates. Lae'zel could do it to spare Orpheus. Minthara wants to usurp gods, and could see it as her ticket. Jaheira's got a history that would make her primed to sacrifice for everyone. Minsc would just be funny.