To be honest, there's kind of a limit to what you could do with them now. As other people have already said, their character arcs have pretty much already been done. Maybe they could help the CMC solve a cutie mark problem one of these days?
Best plushies: 4DE, hooves down. I've got an adorable snuggly Fluttershy from them, and she's so nice to sleep with! Some fanmade plushies are really great as well.
Worst plushies: Hasbro, definitely. They are objectively trash.