The shaker motor was a good idea. Putting it in games other than Earthshaker was also a good idea.

The way the magnasave works on Rick and Morty
The way the loop shot into gold targets works in Pirates of the Caribbean JJP. The more loops you do before hitting the gold targets, the more gold you get.
The way character selection works in PotC JJP.
How Plundering works in PotC JJP.
The way the position of the Powerball in the game matters in Twilight Zone
The way there's a map of modes that you progress through in Jurassic Park Stern, and the path you take through the map matters. It doesn't have to work the same way, there are other ways it could be implemented.
A multiball you build towards with switch hits, like in Elvira's House of Horrors.
Side loops that end up on one of the lower flippers, like in Godzilla Stern.
Shots like the one in Meteor where it ends back up on a flipper.
The customizable video mode from Bride of Pinbot 2.0
Lenticular images like on the backbox of Dr Dude.
This one you guys might think is crazy: Having the upper flipper controlled by a separate button, like in Heist. The pinball playerbase hates staging but doesn't realize it. I watch footage of top players and more often than not they don't bother to stage in situations where it would obviously be useful or they stage poorly.

I used to say the tilt warning lights, but now they're in PotC JJP, Guns n Roses JJP, and John Carpenter's Halloween. So designers other than Mr Meunier are using them.
PS:
In a way, the different floors of the sinking building on Godzilla Stern harken back to the rotating diverter on Gilligan's Island.