In vanilla Minecraft, Skeletons don't target villagers. Savage and Ravage introduces Skeleton Villagers, which are hostile to both players and villagers. I suggest two ways of making their behaviour more consistent:

• Skeleton Villagers are hostile towards villagers but neutral towards the player. That way it fits with vanilla skeletons being hostile towards the player but neutral towards villagers.
• Change vanilla skeletons so that they also target villagers.

You can decide which one of those approaches is preferable. Config options could also be made for players to customize this behaviour to their liking.

Nothing inconsistent about the way they currently work, this is just a different interpretation. Vanilla skeletons target players, and Skeleton Villagers target both due to their appearance as a villager.