In the dev update video there's a sign in the back that says animation with the Multiversus logo
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This combined with Powerpuff Girls, Dexter, and Animaniacs content leads me to believe seasons will have themes and that animation will be season 1.
As for roster theming not lining up, I don't think that'll be an issue. First off, I think Multiversus isn't gonna count Joker, BG, and Jason as "Season 1" characters, they'll be treated as launch characters. Secondly, for future characters I think that while the MAJORITY of season characters will be themed to the season, they'll leave one or two extras that don't relate to it. The season theme will mostly focus on dictate stages, cosmetics and maybe events.
I don't think it's a bad idea if done well, giving seasons themes could be a good way to make sure the speculation scene doesn't become too stagnant with the typical top choices, every season will give incentive to take a break from the most popular choices and get people to think "ooh! this character would go great with the space season!" Or something like that
I also reckon they wouldn't make seasons themed to specific franchises or studios. They'd do broader categories like the above mentioned animation and space.