ORIGINAL: Jonathan Palfrey
I think "balanced and historically plausible" is in general a contradictory objective. Most historical war situations were not balanced.
Nor, oftentimes, are they fun. Nor, in the end, historical. Antietam: "General Burnside, take that bridge, now!" Union routs ANV. War ends. That's completely historical in the sense that it could have, should have, happened given the balance and disposition of the forces involved. But it's completely ahistorical in terms of what actually happened. So when you ask for historical fidelity, which history do you recreate: the outcome or the potential?
However, as Roger has suggested, you can balance a game by adjusting the victory conditions: in this case, the Confederate player can be awarded a win for doing better than the real Confederates did. That's sensible; and in fact FoF already implements that idea in effect, by awarding the Confederate player extra victory points from 1865 onwards. (Full marks to Western Civ for this rather neat idea.)
Yes. But then you end up with a glorified game of pinball. "Woohoo, I got 1000 points!" The bane of most "historical" wargames.