I was thinking about replacements, and how 'generic' they seem to be. Recruit some troops for replacements, and they can be deployed to Missouri, or end up in Virginia, depending on your immediate need. I replacement is technically a virginia, a south carolinian or a texan, as they can replace any single state unit.
How about if each state 'regiment' was a specific unit type (i.e., Missouri Cavalry, instead of just Cavalry), meaning that your replacements will only be useful for that state's forces (you buy Missouri Infantry Replacmeents, which are only usefull to fill the ranks of Missouri Infantry Brigades).
However, this would create the need to have multiple models for each state designation of a 'regiment' (i.e., instead of 5 Militia Models, there has to be one for each state).
Possibly it could be divided into regions, western, and eastern, meaning that you buy replacements only usable in Eastern Brigades, or those only in Western Brigades.
This would result in a more realistic form of replacement production and deployment, as maybe your Eastern forces recieved more punishment than your western ones, and you just don't have the Eastern replacements to cover the losses.
This way, an infantry replacement couldn't be immediately deployed anywhere given the need, but is limited to geographic region.
your New York regiments would only take New York replacements, wouldn't they?