I understand where you're coming from with the parallel, but for the sake of understanding what's going on here, it's worth bearing in mind that they are not really equivalent.
Potts (at least as far as I can tell from the movies; I haven't read the comics; please let me know if they take a different approach) is personal assistant to the cranky genius; her job is to go with him and help him do his next great project.
Shotwell is operations; her job is to take over the company the cranky genius built, keep it running smoothly and profitably, and let him go off and do his next great project.
Different jobs, both important. (It's a pity Musk doesn't seem to have a Pepper Potts, who might have talked him into giving up his Twitter account.)
> ... her job is to take over the company the cranky genius built, keep it running smoothly and profitably, and let him go off and do his next great project.
I think this is precisely what Pepper Potts ends up doing in the movies. Tony Stark stops running the company. Not to condone the comparison or anything, just clarifying what happens in the movies.
Gwynne didn't "take over a company a crank genius built"... she helped build that company with her own genius and A-grade aerospace experience.
I am not calling you out specifically... just think that her importance to SpaceX has been diminished and undersold and I think it due to: (1) the oversized spotlight that Elon commands and (2) Gwynne is a woman, and fairly attractive at that... and so multiple biases play against her.
I had to look this up, but according to both their wikipedia pages Shotwell was born two months after Pepper Potts first appeared in the comic. In 1963.
(Comics are not nearly as original or modern as they'd like to pretend to be!)