For some reason, the animated shows just get episodes for the premiere and finale and sometimes maybe mid-season.
I've assumed there's a higher budget for the live action shows to fund this extra content.
Maybe they're using some of the Prodigy promotional budget towards other content, like the Instagram Mission Logs as well as the weekly "Set a Course" and "The Science Of" videos. It does appeared that the weekly videos would have integrated well into the breaks if there were more "The Ready Room" commissioned for Prodigy.
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