I'm with Joe on this one. Personally though I also think it was a bit of a power play. Since the war was such a recent event I have a hunch that it might have been a power play as well. I mean think of it this way, adopt the saddle idea of a Yankee and make it the universal design for everyone, even the Southern states? Seems like a bit of a smack to the face to me...
But yes, they are odd to ride in. I rode one recently at our frontier army days at Fort Lincoln and have ridden in more comfortable and less comfortable saddles. There are definitely better choices for long distance riding :) Like if you do want to go Civil War I would look into a plantation saddle. Classy, comfortable, and designed for long hours of use. Also, after the war, ladies were no longer the only ones riding aside, many men that lost legs or sustained leg injuries rode aside because riding astride was no longer possible.
I know a place where you can get a custom built McClellan for a decent price. It won't be vintage, but it will fit your horse. It will also not be so awfully uncomfortable, and once you put your blankets and bed rolls on you probably wouldn't have enough people looking close enough to notice that you are actually more comfortable then them
Here is a link to the McClellan I mentioned... http://www.sycamorecreeksaddles.com/MAC010-A.jpg