I think there's space for deep cuts even in a film. For instance, I think at some point (in the series, not this specific film) a "inside the mind" sequence would happen, and I would love if they retooled Dream's Deep for that purpose. (Its like, one of the defining Dream Team setpieces and the game criminally underuses it.) Not everything has to be taken from the most popular entries, especially when people know superfans are looking for deep cuts.
I don't think there will ever be "release a new movie to tie into this new game" scenarios. Movie production and game production operate on different timescales, nevermind the differences in releasing movies compared to releasing films. It would be way to easy for two products to fall out of sync if they tried in one or both of content and release timing. But I do think there are so many Mario stories that they really aren't going to run out of things to adapt/reference from the main series, especially when games release faster than blockbuster films. Super Mario 3D World? Secret underground civilizations are a dime a dozen. New Super Mario Bros. U? Its a "the bad guy won at the start" story. Super Mario Bros. 2? Like I said, dream sequences are well versed territory. And Super Mario games have only gained more story elements as time has gone on, thanks to technological advancements allowing for grander cutscenes and maps. (and then we have to account for the inevitable shared universe with Donkey Kong, which will slow down the rate they use up Mario material by allowing for use of Donkey Kong material and by reducing the rate they have to produce Mario centric films.)