To be fair, it's kind of difficult to improve the core combat mechanics once the game's gone gold.
I honestly can't think of any way to significantly improve
Witcher 3's combat after the fact. Adding enemies and weapons with more varied move sets would help, but I don't know if the game has the proper framework to support those mechanics. I think the reason mutations don't improve anything is because there's simply nothing else CDPR can do that won't completely alter the game's balance. As proactive as they are in their expansions, I doubt CDPR would feel comfortable making potentially game-breaking features after release.
At least there's a few mods that could help, though.
This mod (as well as a few others, but I like this one best), is the best attempt to fix the game's combat/leveling/loot systems I've seen so far.