This mod completely defies the purpose of two handed weapons. The reason that they're called two handed weapons is because the NEED both of your hands to use effectively.

How about duplicating all the weapons in the Creation Kit? Then you'll have a craftable variant for duel wielding and one for two handed usage, then you can just lower the swing speed and damage on the duel wielding variant. Turning down the stagger multi might also be a major nerf for it, since I'm pretty sure they still deal the stun damage they do as two-handers.

And ofcourse then, only adding the "true" two-handers to the leveld lists, that would also stop the hordes of people complaining about it looking wonky on NPC's :3

Alsoalso, I'm very curious as to how you actually did it. I've been trying to recreate it with some weapons from mods, in particular Jaysus his mod, according to the Creation kit window it should work, but the weapon stays invisible in my right hand. it does show up in the left hand though.

The thing is the only mobs that should be using two handed weapons are ones that would originally use two handed weapons, NPCs that would normally use one handed should still only use one handed weapons. I have been thinking about just making it so that "boss" NPCs use two handed weapons but I fear that they would become very hard to find then.

About how I mod the weapons. I don't have my work flow chart infront of me and I can't remember the process of the top of my head. Some things that you may be doing wrong though:
Make sure your attack animation is set to the proper weapon type; a two handed mace should be useing OneHandMace Anim Type.
Make sure Equip Type is set to EitherHand.
Make sure your Model and your 1st person Model Object are the same (this is likely your problem).

Then it is most likely the 1st person model...
I remember from modding Fallout NV that I could extract the files for such things from the .BSA files, or they might be included in the mod files in the data folder, I'll check that then.

Also as I said, maybe make the duel twohanded craftable? And just hand pick a few bosses to give the duel wielding two handers to.

I don't think this needs balance. This mod's purpose is to use 2h weapons in one hand. There's no need to use it if you think its OP.