One thing I think would add a lot to Dominions 3, and yes, it's greater variety.
A few more terrain types, special terrains if you will, to allow greater diversity and tactical/strategic nuances in maps.
True "Port" provinces, which would allow sailing to other ports but would
not be usable by fliers. (This might also be done via a new type of
neighbor command.) Reason for this : currently maps which attempt to implement ports are abusable via flyers, a la Cradle of Dominion. In addition, I think strategic movement should both begin and end in a port - ie, cavalry can't move across a sea and extra provinces beyond.
Chokepoint provinces : land provinces that can't be bypassed / flown over.
Portals : to allow movement to another portal, but without the provinces being considered neighbors for purposes of scouting, dominion, castle admin, etc. These could be two-way or one-way, and require a troop to at least begin movement on the portal province.
Another variation on "neighbors", to indicate provinces which aquatic / amphibian troops can cross between, but which non-amphibians can not. This would solve some issues with maps using rivers/bays/lakes as barriers between provinces, where logically amphibians should be able to go across. (Also possibly for flyers to cross - a half-mile wide river might be a near-complete barrier to infantry and ground troops, but not to flying troops.)
I'm sure there are other possibilities others can think of, but these would really add a lot to facilitate the ingenuity of the Dominions community's mapmakers.