Here's another suggestion: after completion of The Undead Legion quest, it is pretty silly (and annoying) to still see hordes of undead legionnaires patrolling the countryside. After completion of the quest, there shouldn't be any undead left, with the exception of zombies and ghosts. I realize that would probably involve a lot of scripting, but how about a balance.txt file (if that is where the data is) that just removes them?
Upon completion of the Legion quest, the altered file could be substituted for the vanilla one. Then, when playing a character that hasn't done that quest yet, the original file could be reinstated..