I feel like I'd draw a distinction between the Minions problem and the B.E.N. problem. B.E.N. is a problem with the story and the character himself. Minions are solely a problem with marketing, imo? Like, in the movie they stole the show, but they're 100% exactly what they're meant to be in that movie, and they do it well. The minions are good mascot characters who then got pushed so far as to become obnoxious outside of the movie.
I have 8 My Little Pony plushies, but I don't want a Grunkle Stan plushie. I don't think that's a failing on the part of Gravity Falls as compared to MLP; that's simply a matter of some characters lending themselves to merch better than others. (As an aside, I'm very behind on episodes but Waddles from GF seems a good example of a background Animal Mascot who doesn't contribute to the plot, other than his importance to Mabel, but also doesn't become obnoxious)
I mean, heck, GIR has the same problem the Minions do. It's hard to find any IZ merchandise without GIR yelling about tacos on it, and GIR's creator has expressed frustration with the way GIR's ~wacky randomness~ is the focus of all marketing. That doesn't make GIR a bad character in the actual story, and it doesn't make IZ a bad cartoon, but it does make me yell about how we don't need any more GIR hoodies the same way I'd yell about how we don't need Minion hats.
So like, the way to avoid making Minions' mistakes is to not make spinoffs of the most popular character in your story and avoid advertising their mugs on every brand of cereal, which, I think shouldn't be too hard for most of us to do. But to avoid making B.E.N., we have to pay attention to the character's role and personality in the actual story.