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Well, if we're talking hypothetically, then those aren't bad ideas (although they border on anime filler territory). But if they're treated as afterthoughts, then keep them optional like the USUM sidequests.

The problem is that once you remove the dozens of grunts, not that much happens in the story outside the very climax. Getting rid of the grunts would mean coming up with a more immersive story, and Game Freak haven't shown that they're capable of that (no, cute cutscenes and information dumps...