Skeletons aren't alive nor sentient, so its not like giving an orc better weapons and armor. A skeleton is a skeleton, and its stats listed in the Bestiary is how they are in combat, no matter how they are equipped. If you want options in skeleton design, you either need to give it a template, pick other skeleton like monsters or make it a variant monster. I'm not saying you can't adjust AC with better armor, but the skeleton is hardly different.
Skeleton is actually a template unto itself. If you want tougher skeletons, you make it a skeleton of a tougher creature when it was alive. A Skeleton of an ogre would be tougher than one of a human. I don't think non-sentient undead, can intimidate anyone. A vampire could use intimidate, a skeleton, not so much.