Yeah, characters not having a compelling arc being bad isn't a particularly unique thing. What I fail to see is a reason to assume that's going to happen here when all our information amounts to Thor, Jane is Thor too, and Valkyrie is there and still Queen. None of those facts mean Thor can't have a compelling arc, or that he's being replaced.
Why assume this movie is mainly to serve as establishing Jane as the new Thor? What reason do we have to assume they'd suddenly kick Hemsworth, who has never been more popular as Thor, to the curb?
Last I checked, there are a lot of Thor comics. I doubt they're all about being king or being the only one with lighting powers. If the character can no longer be compelling if he's not king (something he was not until the end of his third film) or the only one with his powers, then that would reflect poorly on him as a character. It'd be like asking what the point of having Batman in a Batman movie is if Robin, Batgirl, Nightwing, Batwoman, Spoiler, Huntress or some other Gotham vigilante was also in it. And like those characters would likely have arcs that would be designed to challenge and flesh out Batman if it's a Batman movie, I'm sure Valkyrie and Jane's arcs will be set up to challenge and develop Thor as well. I see no reason to think Waititi suddenly can't write a protagonist.