No really, though we have some house rules. We don't replace leader casualties. We considered (and forgot) to give +1 for combined infantry/cavalry assaults. I find at the grand tactical level it works quite fine without a lot of changes.
We also don't replace leader casualties in the ACW, since it seems that both sides operated with a shoe-string staff compared to later European armies.
For Waterloo, we had heavy artillery (12 lb) give a column shift when firing. There are some other house rules from another group in the Yahoo group files, nothing too major.