A few notes:
1. This clearly needs more time in the oven. I'm not going to make any changes on this until next week at the earliest, so please feel free to keep discussing, this is good stuff.
2. I'm now leaning a bit more against the "lots of customization" thing. It's true, this would just encourage players to specialize
less, and to try and recreate the same character repeatedly. Which, while attachment to ones' character is good, the former is actually detrimental to gameplay so that's not so hot.
3. I really prefer Jerebaldo1's suggestion on dexterity and how that would work. Regardless of how the rest of this goes, I think that makes a lot of sense.
4. Penalty for death is something that can't really be nailed down until how the whole character-creation stuff works settles down. It's like building a house, you have to have the foundation before the roof. Permadeath consequences are of lesser importance to me than the other stuff here, so those get decided on last. Same thing with boss drops. As we start including more and more spellscrolls, it may be that bosses simply drop spellscrolls.
5. Customizing NPCs that you find is definitely flat-out-no. That really makes it feel completely wrong in my opinion: this is somebody you met, not somebody you designed.
6. That said, having a stable of characters in your settlement that are all useful and that you can switch between sounds really good to me. My thought is that there would be some sort of "retirement" scroll that you could get. Using that in a settlement would abandon your character but leave them alive and in the settlement, with a profession of "Retired Glyphbearer." So you couldn't use this to game the system and get NPCs of other professions. But you could use it to retire one character and create/choose another one, then later swap between the two of them.
7. Clearly there's a desire for more customization than we now have, and also the fact that you have to collect upgrade stones at all is an annoying grind at first and then pointless. So that needs to be solved either way. But there also seems to be a strong desire for some randomization and for the game to make you have to play outside your comfort zone, which I also am frankly a little relieved to see.
8. Perhaps, therefore, the past idea of just having a "re-roll characters" button that you can click is a better thing. And then it gives you something like 3 choices always, completely at random. And you get to choose a name for them, and allocate some extra stat points to them rather than having the upgrade stone business (so, still a new character selection screen, but not build-from-scratch).
9. It strikes me that if people can't play as their favorite time period, there's going to be some problems because they may have their enchants and spell unlocks built around something that is then inaccessible. IE, if they are geared to a high-mana strategy and cannot get anyone with high enough mana that could be enormous trouble as they are then basically stuck.
Clear as mud, eh?