I've counted a lot of regiments. By late 1864, the number of regiments each side will have built will be roughly accurate. The number of men per regiment is too low in the beginning and too high in the end of the war - the game doesn't allow the max number of men per regiment to vary and the player will want to keep each regiment at full strength. By the end of the war, many regiments could be treated as battalions (groups of 3-6 companies) in terms of size and maneuvers.
As I've said, the regiments involved in what I consider the early war big 3 of battles (Bull Run, Wilson's Creek, Shiloh [which was early 1862]) are nearly included by event with enough economy to build forces so that all three battles could be fought at roughly the correct strength. After this, continuing the game your regiment count usually (always?) falls behind what happened in real life for 1862 and 1863. If you want to change this, you could make a mod to add a couple events or decisions (perhaps call them 300,000 more) which give you the WS, Conscripts, and money to grow your army more in those early years (by 1865, your force pools will be exhausted even if you have the resources to recruit more men). The trick is that such changes should be applied equally to both sides. If you make this change, I'd also recommend turning down Athena's aggressiveness, as she's likely to send the extra CSA units north I think.
I've never played the 1862 start in AACW (and don't have the extension for CW2) and don't have any idea about it. To me, it sounds like a lot of work for the developers to set up the 1862 start true to size. If they did it, that sounds wonderful. If they didn't, I agree that it wouldn't be a very fun scenario when you could just play the April or July 1861 scenario (waiting for divisions isn't that bad).