Countering Villa + Jeweler in Puerto Rico: The Nobles
Ultimately, we decided that Jeweler and Villa shouldn't be allowed in the same game.  Since the first expansion already has the rule that the Hacienda and Forest House shouldn't be allowed in the same game, there's a precedent for this.

Villa + Royal Gardens is still a bit of a problem, but with Jeweler out of the picture, you won't be getting obscene amounts of money from all of your Nobles during the crafting phase.