3.1 personally I'd be happier with them fixing the current trait system and ideally having that and your traits and your actions towards them being the thing that impacts most on Nobles interactions with you.
3.2 I agree, but by having characters as archtypes you'd need to make the quests and dialogue unique/random because as soon as quests or lines got repeated I think it would ruin the immersion to have all archtypes the same.
3.3c is a great idea, the rest don't add enough to the average game to be worth implementing IMO.
3.4 Wholehearted yes to everything with the exception of 3.5d as I don't think the outside focus scans and would keep it faction neutral. Love the garden idea especially.
3.5 Again agreed as a trait rather than a blanket rule would be a great feature and the best way of implementing this issue. Also a good way of giving nobles more personality too.
3.6 I think the entire concept of smithing as a player clashes with every other element of the game and should be scrapped and replaced by 3.6.i. which is a great idea and I would use. Would be good to apply to armour and ranged weapons even if you couldn't craft them to the same level of detail. If you are going to keep it though I am personally not convinced about the changes you suggest, although they would flesh out the smithing as the focus of a play through, I can't imagine myself every wanting to do that playthrough, so again would rather they devoted their efforts elsewhere.
4.1 & .2 I am indifferent on
4.3 Hell yes. Hate fighting in villages and the uncertainty of when you will be in one or not when in the map.
4.4 Again yes it is a little jarring and would be great for them to fix to give them more of a rabble like approach.
4.5 Low priority and I can see how they could get hard to balance the more you add, but more options are good.
4.6 I don't play multiplayer so have no opinion.
4.7 I'd be happy just being able to drop in as a single player character into someone's campaign/sandbox and help them out, but the fix you suggests seems good too.
4.8 Agreed, but you'd need to make them a bit better than they currently are to be worth the investment.
4.10 Agreed cautiously they can be a little dull if you are forced to move around too much in them. Just implementing the gang features better might be a better solution here
4.11 It would really just serve as a bit more of a random RNG so not bothered personally.
4.12 Would rather just give them a home town rather than a distinct base, but have that move based on which faction controls it.
again some great ideas thank you for sharing.