I've compiled a list of the changes I'm making in my own game. I would like to see many of these in the stock game, but I'll gladly settle for being able to continue to modify the game. None of this requires changes to the engine.
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ATHENA GETS BRIGADES, HUMAN PLAYER GETS REGIMENTS
It's been said that the AI can't handle creating effective divisions from single elements/regiments. During an event, there are ways determine if a faction is being controlled by the AI (CheckAILevel, CheckIsPlayer). When the unit pools and brigades are created, the event checks whether the faction is human or AI. If AI, unit pool has few changes; most standard brigades that are created by event remain. If human, player gets mostly regiments in its pools; fewer (if any) brigades created by event. Iron brigades 1 & 2, Virginia mega-brigades, etc: gone for the human player. Some brigade sizes are reduced. I try to achieve a match between in-game total element count (including elements making up brigades) compared to historical force composition and size.
DIVISION CREATION ALLOWED AT START OF GAME
Brigades and divisions were formed by both sides from the start of the conflict. It is possible to keep the ability to form divisions at the start of the campaign from being abused overmuch by reducing the number of divisions available to a faction until later in 1861. It was done that way in AACW. Number of divisions available will depend on human or AI control and faction. I'm still playing with these numbers.
UNIQUE REGIMENT NAMES
In vanilla, there are many duplications. Some of this is cosmetic, but some of it should really be addressed. For example, in vanilla game 71st New York shows up at 1st Bull Run, and then again in the Excelsior brigade. This gives units at no cost to the Union player (most of the flavor brigades come at no cost). If the Union side is controlled by the AI, and the Excelsior brigade is created, any pre-existing elements included in its creation are removed from elsewhere on the board beforehand. The issue of free militia via training to regulars still exists, unfortunately.
90-DAY VOLUNTEERS MUSTER OUT
A signficant portion of enlistees from the first Bull Run mustered out in August. Some of them reenlisted, but that organization took place in their respective home states. I identify as many of the 90-day regiments and other short term enlistees as I can and disband them approximately a month after their historical date. I would love it if the game had built-in time-periods for some units. It was regular practice for NY regiments to enlist for 3-6 months for volunteer duty near the capitol. It's too much for me to keep up with a regular rotation of short-term enlistments. I'll only be focusing on the original 75,000, and a very select few others.
LINCOLN'S CALL FOR VOLUNTEERS CREATES CONSCRIPTS, NOT MAGICAL MYSTERY BRIGADES.
There are many silly 3-element brigades that don't correspond to anything IRL, especially the regiment names. There are also militia units that show up that are fictional. Gone. Instead, only the AI gets a few brigades that were created as such near the beginning of the war. After that the AI is on its own, creating most brigades from scratch. Some regiments were organized and funded by individuals or at the local or state level. If I can find those, there are no or reduced resource costs. Any nationally organized and funded units (e.g. the Regular Brigade) will still be created by the AI, but there is a corresponding resource cost. Stannard's Vermont brigade was only a 1-year enlistment. It's silly to give free elite infantry brigades to the Union for years on end.
SUMNER WAS ON THE BEACH, NOT ON THE PLAINS
Many units are moved around to facilitate someone's or many someones ideas of what would make gameplay easier. As of A. S. Johnston's defection date, Edwin V. Sumner should shortly thereafter appear locked in San Francisco, CA. Even if you argue that he was Dept. of the West commander in Kansas before the war, he went to DC for Lincoln's escort duty and was there on his promotion date in April. Tanning with Sumner in California are at least half a dozen batteries of US artillery. Some of those never left San Francisco during the war. Several other batteries of regular artillery started at seacoast defense forts, mostly in Florida or at Fort Monroe. Benjamin Butler effectively starts his military career by suppressing the riot in Baltimore, MD; not at Fort Monroe.
I change these and numerous other unit-level starting appearances. I even got the "1000 federal troops" and artillery and the appropriate units (6th & 8th Massachusetts) with Butler. I was kind of proud of that.
LIES, DAMNED LIES, AND COASTAL FORTIFICATIONS
I already have a thread on the proposed changes to fortifications.
http://www.ageod-forum.com/showthread.php?38072-Forts-and-fort-artillery-changes
In addition I am adding a few cities and settlements, and relocating or renaming a few that don't make sense. I won't go into it here, but I will say that Camp Dick Robinson goes back to its original AACW and historical location in Kentucky. It wasn't in Lexington, sorry. It wasn't even on the same side of the river as Lexington.
I AM THE VERY MODEL OF A MODERN MAJOR-GENERAL
The ranks in vanilla CW2 really annoy me. I've cobbled together changes that aren't very refined but they work.
Union: any *Union* leader rank 2 and up has his model's ImageId set to the 2-star version, with the exception of the General of the Armies or General-in-Chief. This has no effect on gameplay, and is ignored by the function displaying the number of stars on the leader's army graphic on the board. But I find it so soothing that I can't play the game without it. I am thinking about other Union General-in-Chief changes. Jefferson Davis acted as his own GiC, but Lincoln relied on an appointee. Halleck didn't command in the field after his promotion, but both McClellan and Grant did. The engine limits what I can do. I can't make Grant commander of multiple army commanders. If someone is promoted as the in-game "General-in-Chief", it has no effect whatsoever on the Union armies as a whole. The player is the GiC, but the game still simulates the Union promotions in a half-ass way.
Confederate: The engine imposes one framework on all factions, and the Confederate faction is less able to fit into it. In my games, it seems like CSA leader attrition is almost always higher than Union. There's no way to properly represent brigade commanders under a division commander. Some divisions and corps were temporarily commanded by brigade and division commanders. If a combined-unit commander is incapacitated, the combined-unit (division/corps/army) completely falls apart. The game doesn't model command hierarchy beyond a basic level that's necessary to organize division/corps/army. You can't designate spare generals in a stack as backup commanders. You can't designate any other hierarchy of command. This might be hard to code but it would be very welcome.
To deal with the perceived higher leader death chance of the Confederate side, I have pushed up the dates of most commanders on both sides to their brigadier promotion dates or first appearance dates; as you know, some commanders started at higher ranks than brigadier. Many of the Confederate commanders don't appear until their promotion to major general (but they still start as brigadiers), which commonly equated to division command in the CSA. With more generals available earlier, if Zollicoffer dies in 1861, the Confederacy isn't crippled for lack of commanders until E. P. Alexander spawns (at the wrong rank) in January 1862.
I am considering changing the ImageID field for CSA leaders (corps command was usually limited to lieutenant generals, etc) but I haven't gotten around to the research yet.
Since I don't change historical unit pool sizes, more leaders for the Confederacy does not mean a correspondingly higher number of 18-element divsions. The only way to do that would be to leave virtually no garrisions anywhere and have divisions composed of lots of militia. Possible, but also possibly unwise.
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That's all I've got for now. I'd like to see some other changes (3" ordnance rifles alongside 10lb Parrots, both wind and steam-powered ocean-going ships with different costs, ad nauseum), but I haven't started implementing them.