Definitely love the theme!
I can think of ideas like "the voice" mode where it causes havoc on either the ball or your flippers. Also modes that include the thumper or "walk over the sand dune" where you have to make alternating ramp shots. Maybe a mode about a crysknife. I'm not sure how far the 3rd movie will go in the Atreides lines after Paul (e.g. Leto and his sister) or will it stop at Paul becoming Emperor. Could also include an interesting mode with Paul's sister Alia who went a bit "mad" (abomination).
Since there are a lot of interesting characters in the series, you can have a mode where the player "collects" characters after completing a mode. Similar to how Indiana Jones (Williams) pinball has characters you collect.
While I know you already have the central toy being Feyd-Rautha, but having a sand worm as central might be more visually interesting.
I think with pinball tables and themes the question is -- what role does the pinball player have and what role does the ball have? If the player is using the ball to advance scenes and main stories points in the movie, then having the Ball and sand worm could be more interesting. The player can collect sandworm teeth to craft a crysknife which then after X many perhaps you can fight Feyd or kill the emperor, etc. You can use similar concepts as the new Stern D&D pinball table and have the sand worm spit out balls in a multi-ball. You can also use the sand worm as a mode where the player has to "ride the sandworm Shai-Hulud." Doing things like "hooking" the worm, etc. Wormriding could be a means to advance the story since Fremen have to do this to head to the south regions of Dune, etc.