Has the broken stuff like way overpowered weapons via enchanting/blacksmithing been fixed yet?
That is still in-place but how can it be broken if it's the decision of the player to use all three (enchanting, blacksmithing & alchemy) or not. It's not like Bethesda forced us to utilize all three.
Still, if you think that holy trinity is overpowering and you're unable to restrain yourself from not using it I believe there are mods that up the difficulty throughout the game. Deadly Dragon is one that I've heard that makes the current default dragons pale in comparison. --- "You must gather your party before venturing forth" "Go for the eyes Boo! Go for the eyes!"