Come to think of it, this is to be added to the countless things I've mentioned about river/rail/wsu/manpower,etc,etc,etc. being built and handled at national level. For the moment let's forget you have Tennessee building WSU and these WSU go to the pool and you can build a gun battery in Texas without transferring those WSU beforehand... same goes for those conscripts that are produced (with bounties) in NY but you can use them to build militia in Missouri.
Now in regards with unit production and replacement that's an obious limit of this system. Needless to say a son of Virginia wouldn't go to fight for the Army of Tennessee, he would go to fight for General Lee, that means you can't buy replacements at the national level either. All right, as I said, forget it.
The EVIDENT limit of this system is in the transport of troops which really is completely ignoring the HUGE logistical difficulty the generals really had to surpass during the Civil War.
Imagine you have a new bde fresh built in NY. I know this is not the case but just an example. You want to move this bde to St. Louis MO. This is at all possible in CW2 as well as AACW. In reality that bde would have to take a dozen trains (rails on a single line so it's a lot more than the fast travel we see in the game), spend long time and EAT (consume supplies).
The game simulates this with rail point... now imagine a locomotive that goes from NY to St. Louis. Imagine a SINGLE locomotive. How many stops, how long, how much supply it would use for real to transfer that single bde. At the end of the turn that locomotive is in St. Louis... you can't use it to transfer another freshly built Bde from NY to St. Louis... but in the game... you can. That's BAD.
Nevertheless add to this problem that sometimes you'll have troops in transit throughout the turns (between turns a long move performed half on foot half on rail). That unit that is in transfer, has PAID for the transfer the national rail points but at the beginning of the new turn those points are regenerated. So you can actually transfer more than you paid for, to be added to the supply movement by rail.
All you need to think at this point to see why it's such an important change is about the fact every single rail line can be damaged locally and imagine the problems to repair it if the state has few WSU. Also remember that one of the most important changes I think this engine needs is the military control required to let a train pass. I think it should be near to absolute MC.
Would you send a train in a territory where there could be a bomb under a rail or a bridge and you could lose 1000men on the spot?
Transport and supply need to be made more in a realistic way if they are to simulate something properly. The Union and CSA had to overcome terrible logistical difficulties and this engine is well worth capable of handling these problems starting from the transport but I know this is a big decision to make and even bigger trouble to implement (and for the AI to handle).