The potential for adding new content is tremendous. Will it be possible to make separate exterior maps?
That is on my to-do list for post 1.0 development. In fact, very close to the top of that list.
how hard would such a system be to implement, more or less?
Not very. I already started to add various bits and pieces that will be part of the necessary groundwork, when we add this feature (probably in 1.1).
That is, in order to keep the system as bug free as possible and to work with the existing content of the game, the second character should probably be restricted the same time and cell as the first player and, at least at first, not be allowed to engage in their own separate quest lines
Same cell, no. That is not necessary. But all players will share quest progress. There is nothing we can do about it. The way Morrowind.esm is written we simply can not have separate quest progressions for the individual players.
How hard would it probably be to implement multilayer in that form
Medium hard, but a shit load of work.