I suggested changing the per-deck-limit for Mishra's Workshop to 2 or 3, but it seems this suggestion is not really being taken seriously. I suspect the reason for this is the same reason that the DCI used for maintaining a single B/R list for both Type 1 and Type 1.5 in the past: fear of administrative complexity. I can understand that having a max-1-of list, a max-2-of list, and a max-3-of list, rather than just a single restricted list, seems scary.
As long as we are thinking outside the box, another solution to achieve a similar end is to change the parameters of the game for Vintage. @Smmenen has argued elsewhere that it's not unreasonable for different formats to have different mulligan rules. So why not change the 60-15-7 parameterization of the game for Vintage? (60 cards maindeck, 15 cards sideboard, 7 cards starting hand)
It would be an incredible coincidence if 60-15-7 turns out to be the parameterization that optimizes quality of experience for Vintage. The optimal parameterization is probably something else.
Maybe 80-25-7 would work better for the format. It would drop the Mishra's Workshop % to 4/80 = 5%, which matches what my max-3 proposal would achieve, which is why I say this would be another solution to achieve a similar end.
Rather than blue decks having something like 54 core cards with only room for innovation on the remaining 60-54=6, we might have room for innovation on 80-54=26 cards, leading to more diversity.
By having more room for sideboard, there is more opportunity for innovative transformation strategies, and more space to pack specific answers to threats. These things should ultimately leads to more skillful games.
@brianpk80 feels that 1/60 = 1.66...% is too high a density for Monastery Mentor in a deck, and thus suggests banning it. My suggestion would lower the maximum Monastery Mentor density to 1/80 = 1.25%, which is a meaningful decrease.
Philosophically, as long as the card pool keeps growing, I think an increase beyond 60 must be made at some point. Preordain, Ponder, Brainstorm...more cards like this will inevitable come, and at some point, years from now, even if every one mana cantrip is restricted, you'd be able to pack 30 of them in one deck if you really wanted. A format like Modern is always culling the card pool and so will never face the same kind of pressure to alter its game parameterization.