Two Simple Improvements
"Alright Maggots! Archers in front, pikemen behind" (as far behind as possible).
These have been mentioned before, of course, but now that the game is becoming fairly stable and the maps are more interesting, I think a reminder is not out of line. First, it should be fairly straightforward to set a flag on units to indicate melee or ranged and the module that plunks the units down on the combat screen would check the flags and plunk down the melee units first. Second, I have found that the boats can be almost useful now for scouting/colonization. I don't think it would be too difficult to give them one extra tile of movement. These two things, while relatively minor improvements would make a huge impression on gameplay.