A couple I considered:
1. Letting the CSA player choose the location the Capital moves to when it leaves Montgomery. Have penalties for small city size, so players can't just set it up in the middle of nowhere, but I would like theoption to set up somewhere different aside from Richmond. Could provide a boost in loyalty for the state it's located in. I remember in No Greater Glory, I often put the capital in Atlanta, as it provided a more centralized location, and had good natural defenses with the mountains to the north.
2. Completely randomized generals, with hidden stats until they have participatedin battles. Personally, I'd like to see the stats be "fuzzy" until they've been in a good number of battles, meaning, after one battle General John Doe could look like a worldbeater, and you'd see his stats at 7-6-7 or something, but they would be refined after more fights. So while his actual stats are more along the lines of 3-1-4, it would take a few opportunities in combat to actually see that. After his second battle, they may go to 4-5-5 or something. Having that would have to be optional, because I'm sure it would irritate a lot of folks.

3. All generals promotable to all ranks. Even if it was done like my mod, where they just keep the stats and traits from their last known rank. Or perhaps randomization could be added to the process where once a general is promoted past his historical rank, a random +/- 1-2 points modifies each stat.
4. (Some of the) General's traits based on the forces they command, not their number of stars. I just thought about this today, and it makes no sense that someone like Burnside, (Who, as a corps commander under aggressive generals, gave a pretty good account of himself) when he's promoted to 3 stars, gains Dispirited Leader regardless of whether he's commanding a division, corps, or army. It should only apply to him as an army commander as he was dispirited because he knew the job was over his head. Once he tore up his army, he was reverted to corps command and performed well the remainder of the war. Some of the additional traits, like the Quickly Angered should remain, because that's something inherent, and even if the leader has been reduced to corps or division command, he still has the rank to make himself a pain. The stats aren't as important as they are modified by superiors.
5. Leaders lost due to illness. It wasn't only bullets generals had to worry about, some, like A.P. Hill spent more time in the sickbed than in camp. Randomized illnesses could sideline an important general for weeks or months at a time, just as easily as injuries.
6. Injuries to leaders modifying stats. It's hard not to be affected when you've had an arm or leg blown off in battle, just ask J.B. Hood. Make a random die roll to add or subtract from stats when a leader is injured. Seems a bit counter-intuitive to add to their stats, but consider it this way. If a general is reckless and sloppy about his dispositions, maybe the injury would make him a bit more cautious about the little details before a battle, which could increase his offensive or defensive effectiveness. Or, it could make him cautious to the point of indecisiveness, dropping his Strat rating, or it makes him (more) reckless and impulsive, like Hood...but there should be a chance of it having some effect. Perhaps an Injured trait could be added to any general who gets put out of action for a time, that would modify his stats or something.
7. The ability to set up mustering areas for new troops. Either be able to set specific locations new troops are actually built in, regardless of their actual home area, or do like a lot of RTS games, and be able to have them start marching for the area you designate once they're unlocked. It would be nice to have a set location for each theater, Richmond or Annapolis for the east, Nashville or Louisville for the Central, St Louis or Ft Smith for the west. Delay their production time to take into account travel time if you use the option, but it would be a handy addition for players I think. To go along with that, be able to choose what theater your support units are created in. Not HQ units, since I would think those being in the capital region makes sense, but the others should be choosable as with troops, in my opinion, I've had medical units show up in some really odd out of the way places.
There are a lot of tweaks that can be made to AACW, namely in the AI dept, events, and accuracy, but those are things that can be worked on in the current iteration. I want to know what people thing should be included in (lord willing) a sequal to the best game I've played in a good long while. Thought about putting it in the beta forum, but why not throw it up out here, the people who play the game are the ones who need to drive the features in it I think. So let loose, tell me what you think.