I heartily agree with the last part, but note that using bows to shoot over one's own soldiers is AFAIK a historically attested practice. So not something we should forbid. And I mean, shooting over one's own melee soldiers was probably done to shoot on the soldiers engaging in melee with such melee soldiers...

???? I don't understand what you mean ?

Okay, so, if I understood well, it's the same skirmish battles as the basic games.    How are they called ? Otherwise, I'll start to develop my mod the next week ! I chose to name it "Elpis" : Elpis is the personification of hope in the Greek mythology...

Changing unit speeds and giving units more specialized roles. This is made quite difficult by citizen soldiers, and by unit availability by civ, but i believe it is possible. 

The historical reason for missiles not dominating is friendly-fire. One should not be able or willing to fire missile in a melee due to fear of hitting own units. Missiles should be for skirmishing and harassing.