Playtesting is extremely important, even for simple game! You should try as many combinations of startup options as possible - for instance, the combo of two humans and one machine might reveal a peculiarity that is not observed in a two-person game. You can solve many problems by adding more restrictions. Since the scenario is your concept, you are free to make whatever decisions are necessary to realize that concept; if somebody complains, they are free to make their own designs.
Playtesting is the time when you may have to sacrifice realism and favorite theories for playability. Listen to and watch yourself and your testers as the game is played. For instance, you might have included a city out in the boonies, but in the game it never does anybody much good, while still requiring some amount of attention regularly. Lose it.
Game startup can be confusing to players if they all start out with lots of units needing to be told what to do. One solution is to put most units on automatic behaviors that expire in a turn or two, so that novices gradually hear from all the units, while experts can still override right from the outset. Another approach is to make units independent and allow them to be captured early on. Still another approach is to make units come in as reinforcements at preset times and locations. Since players will form their strongest impressions of a game based on its appearance at startup, attention to this will pay off.