Hope I've been constructive.
You have been, and I appreciate the input.
I'm leaning more and more towards the single structure per hex system, combine with the regions planned for 1.5.
Roads preferably placed on the hex borders,
I think some more "cosmetic" roads will be on hex borders, but major roads are going to have to occupy whole hexes. That way units can march through hexes without appearing to clip through structures. I think that could lend itself to some interesting tactical combat in cities as well. In 1.4 formations didn't handle streets very well, but since units fill a single hex in 2.0 they should be able to fight their way though streets in a similar way to a total war game. That could lead to interesting tactical possibilities in designing cities to withstand attack.
Substitute people walking around with sprites in buildings idling or pacing back and forth to give the impression of activity?
Some structures in 1.4 (like the Farm and the Brickworks) had a visual effect of a worker tending the fields, something like that could work well, I think, and be expanded to people wandering around the "cosmetic" streets around structures. As just visual effects they would have a very low computational cost.