Perhaps in the style of Stone Age you should restrict the usage of areas on the board, so that only 1 player can take a particular action during a round (of course with the bonus discs you can always do an action that is otherwise blocked for you). Part of the fun of the bonus discs is using them when you get blocked out and then snatching resources (or other valuables) out from under them. I don't think you want to lose that.
A combination of a certain amount of bonus discs (my gut feeling says at least more than 3, as you'll probably get blocked out a lot more than in a 3-player game with open placement) and area usage restriction could potentially work well I think.

I do not think it would work well with 2 because of the "knock off" mechanic. If you invent something you flat out are not allowed to produce a knock off of that item. It would give the non-inventory a monopoly in its production and would let him produce it at his leisure.