You know you can select multiple units and then right click the tile you want them to exit to, yes? This is not a criticism, I think your user interface ideas are great. But this particular one I haven't noticed being a problem.

I agree. Many of these type game allow a city to have a waypoint were any produced/exiting units will rally. 

A unit with no movement points will pop out with the "V" key, but will then be unable to go back into the city. Very disappointing to lose a city this way, but I chalk it up to one of the evils of war.

Actually... Stardock's other game (Galactic Civilizations) DOES allow you to set a planetary 'orbital insertion' point, so that when you select a ship, it goes to a specific square.  So the code exists somewhere... this gets complicated with the way cities snake out when they grow though, but it could always just 'unset' the exit square if the city takes over the square in question.

While I do use the 'select unit and then select square' thing a lot, one place we can't do this is when the first city is built.  The Sov, and any units stack with the Sov, picks a random unoccupied square to move to.  I'd rather have the Sov stay in the city, and be able to move him/her out on my own, instead of the current situation.