One of the things that was changed and then re-changed a lot in AACW was the way that ships and forts react to each other. Forts were either too strong, or too weak, or naval gunfire could 'nuke' a fort if you had them go back and forth a few times, that sort of thing. I was thinking, that with the release of CW2, we might add in a new feature to settle things once and for all.
Basically, I think you should be able to 'run' a fort with fairly light casualties if you are moving with the river, while getting pounded by the guns if you move against it. The thinking is something like this: say a gunboat can do 10 knots, and the river flows at 5. Moving downstream, your effective speed is 15 knots, compared to only 5 knots when fighting the current. I don't know what the actual numbers are, but that's the idea anyway. This explains why they could run past Vicksburg with few losses, while trying to steam up from the south would get your boats hammered. While we're at it, you could probably also justify river movement being faster 'with' the river than against it.