Hello Nick,
I am always quite excited for new Civil War games coming out. If there's any historical research/input you may need, I am beginning my doctoral studies at Mississippi State University in the fall, with history, with an emphasis on Military History. I will do what I can to help!
Have you ever played Sid Meier's Gettysburg or Antietam? Or Civil War Generals 2? If not, I'd recommend a quick look at those. The Sid Meier games remind a me a lot of this one, as they are RTS without the game building aspect. Purely strategy, (realistic LOS, rallying for tired and wavering troops). The Sid Meier games also had one soldier represent 20 I believe it is, due to the system limitations of the late 20th century. CWG2 was a turn based game released in 1996 by Sierra, which contains unit supply, morale and excellent use of terrain, and some of the best LOS attributes I've ever seen in a game ( though the AI was lacking).
Another game you may want to take a look at is Take Command and Take Command 2 at Mad Minute Games. http://www.madminutegames.com/ Perhaps any and all of these games can provide some insight or inspiration on where you want to take this, or ensure you don't repeat their mistakes etc!
One aspect of the Total War series I always appreciated was the ground littered with the dead bodies of soldiers who fell in battle. Unlike FPS games (like COD or Battlefield) which remove bodies of dead players frequently during the course of a match, you gain a true appreciation of the sacrifice these soldiers make. As a commander, it is your duty to attempt to win with the fewest casualties possible. One way to realize this responsibility is to have as many men as possible represent the fallen on the field.
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I would also like to see the ability to replay the battle once finished, from a top down view as such:
For history gamers (as I am sure many will be drawn to this game), this would be a very welcome addition. I suppose the map could be represented as it is in Supreme Commander, that kind of top-down view the commander has. It gives the player a chance to analyze mistakes, missed opportunities and the ability to develop AARs should one be so inclined. One print screen later and now viewers can follow the battle as if it was an actual historical engagement.
Or time stop moments, such as above. Or "critical moments" in the battle, where major engagements occurred that shaped the course of the battle. These decisive moments in review I believe would add much more depth to the playing experience, and would be utilized to great effect.