This is a summary of the Skype meeting that took place on Saturday, August 29, 2015, where we started discussing the Master Plan. We didn't discuss the actual content yet, but we did list some things that should also be covered in the Master Plan:

Shops should have a purpose in towns, instead of merely being filler. Presumably, this idea would extend to settlement demographics in general.

Exploration:
Magical items such as Barilzar's Mazed Band and the propylon indexes are also forms of fast-travel, and should be discussed during this section.
The Mages Guild network should also be figured out during this phase.
It's interesting to note that the Vanilla fast travel routes make logical sense. There's usually some flat terrain for Silt Striders to move over between two fast-travel locations.

NPCs:
Faction and race tropes should be figured out during this phase. Lampshading these tropes could be done, especially in the case of race tropes. But it should be limited. After all, it's not a trend if everyone's an exception.

It might be useful to go through UESP's Morrowind page to find other things worth discussing in the Master Plan.

For many of these topics, it's encouraged to start the discussion on the forums, to give people time to flesh out their ideas. The skype meetings will mainly be a tool for speeding up decision-making.

And now, some rambling:
Figure out our approach to prisons, especially in areas where the Empire has little influence.
Get rid of the Inner Sea region, and replace it with extensions of the Vvardenfell/Mainland regions. There isn't enough time to transition to the Inner Sea weather before you reach the shore anyway.
The Velothi underclass is rather marginalised, which might be worth exploring.