Team rocket is basically the mafia, and then gen 3 has team aqua and magma, one of which wants to remove basically all water and the other wants to basically remove all land.

I think that's a pretty drastic shift.

Giovanni is the big bad in the early seasons iirc. No clue how the show progressed past that though but there was always a more serious organization looming (ie Team Aqua and Magma, Mewtwo in the movie are the only ones I can think of right now...)

idk for more recent seasons, but i know the xyz and sun & moon arcs had more serious villains (especially xyz)