1. ED-E will stay still and not fight during combat.
2. ED-E refuses to use ranged weapons(Everytime you switch him to "Use Ranged" he will change back to use melee)
3. He has a reference ID from a mod. I know this because when you click on him in console it displays a REF ID starting in FF(Right now hes ff001a89). Spawning any version of him(Regualr, upgrade Armor, and upgrade gun) will all spawn him with a REF ID indicating he is from a mod.
I have lonesome road installed but that dosen't touch ED-E, the only other one I have is something called ED-E heavy weapons and disabling that does nothing.
1&2 are most commonly caused by him not having the proper gear he is supposed to have, but I checked and he definitely has everything.
He also has some non-vanilla dialog options like "Let me access your multitools" Which opens a workbench and "Could you help me craft some ammo?" Which opens an ammo bench. From what I heard I beleive these are supposed to be usable after you install lonesome road. But when I unchecked Lonesome road in the load order they were still there and so was the strange Ref ID.