AI is really the best way to increase difficulty. Enemies that block better, use cover, heal more intelligently, use wider variety of spells, etc. etc. would appropriately increase challenge for all builds.
Skyrim right now just doesn't have any balance to even build on though. Almost every aspect of the combat has severe issues, and balanced difficulty settings would be pretty much irrelevant when the rest of the combat is such a mess in the first place. Enemy and PC health and damage values are just all over the place, the armor system is just bizarre, skills and perks are nowhere even close to eachother when it comes to relative usefulness and/or power, etc. etc.
Install PISE it tries to do all the things you listed to make the game harder. It removes someof the enemy scaling, makes the loot a lot less cheesy and autoleveld. Improves combat AI of enemies and increase spawns.
