The first idea is a %cap on just how much your character can improve with one tool. I'm thinking this can be done via an MCM menu so players can decide themselves, and the default can be something like 20% or so.

The second idea is making an SSEdit patcher or utilizing SPID perhaps, to give some bonuses to mid-high level npcs. I'm thinking they can start getting bonuses around level 30 or 40. Level 70 or 80 characters can reach the 20% bonus cap, but I'm not sure about the exact balancing to be honest. In a perfect world, this too would be adjustable via an MCM menu, but I think that might actually be too much to ask.