The sieging really feels like a Seven Years War game, especially if you play this game while reading about the wars of Louis XIV, Louis XV, and Frederick II. The flow of the war in FoF is almost exactly how I'd picture the flow of a game based on that period to go. It's not off-putting exactly, but it doesn't feel like the Civil War. The AI CSA is clever to avoid pitched engagements in the context of the game (especially in the west, where they can't come close to matching Union numbers), but it's odd to have Grant go 3+ years and never fight one single engagement with a foe possessing more than 20k troops.
In the game context, the problem I have with the sieges is the extraordinary casualties. I had 30k man corps lose 6k men twice in a single turn on a Level 2 fort in Kentucky with a total garrison of around 4k. 12,000 casualties would be a major Civil War engagement and are on the level of casualties suffered at Petersburg and Vicksburg, where the garrisons were many times 4,000 men in size. I can almost buy the sieges as being abstract events that represent how hard it would be to subdue certain areas (avoiding a blitzkrieg), but I can't buy these kind of one-sided Union losses outside of combat (both sides suffered high non-battle casualties from disease and desertion, but only I suffer these abstracted siege losses since the AI really isn't besieging any major forts).
In the beginning of the game, the prospect of siege casualties keeps me from doing anything in the West, because I don't have the camps to replace the men.
I sort of feel that the forts and sieges are kind of a "clock" device, that keeps the war progressing at a semihistorical pace. If the Union blitzed through Kentucky, Miss., and Tenn., the game wouldnt' feel quite right. And if the AI won't fight in the west, that's exactly what would happen (arguably, though, this is exactly what did happen when Buell and Rosecrans were removed). Still, when one pictures ACW operations, you don't usually imagine massive siege trains and huge fortified cities located where Memphis, Little Rock, Knoxville, etc. are in the "real" US.
I love the game. I love the generals. I like the economy (though something really happens to Union money production around the start of 1863 that I can't put my finger on). I find the quick battles more logical than CoG's results. I just think it doesn't feel very historical for the war to be built around sieges.