I don’t think I’d call D&D a consistently great base to start from, honestly. For certain settings and genres, yeah, but others are seriously harmed by trying to make it fit a fantasy adventure system. Mysteries and heists are forced to include a lot more gratuitous fight scenes just to balance all playstyles, for example.
Similarly, I worry that using d20 as a one-size-fits-all will reinforce comfort zones than expand them. Why would a person play the Star Wars FFG system (which I prefer) when they can play the Star Wars d20 system instead and not have to learn new rules? And if you’re making a new system, then you clearly need to include six core stats, because RPGs have six core stats in them, right?
D&D isn’t bad, nor is homebrewing D&D for a new setting. D&D as an assumed foundation of all RPGs can be a serious issue.
Just off the top of my head, you could give them a flaw that, while it doesn’t make them any less cunning, it does let the players see what’s happening.
Method 1: Gloating. What is the point in being a genius if nobody ever notices? When the villain has the party on the ropes, have them point out moments of the plan that the party could have noticed but didn’t. Maybe they wait to give the shopkeep the bounty until the party can see it happen, just so they know.
Method 2: Worse minions. The plan is amazing, but the people carrying it out aren’t quite as discrete as the villain. Maybe the security make a little noise as they stalk the party, and there are moments where the players could spot them.
Either way, the players will know something is up, and might have an opportunity to use this new information to turn the tables on the villain (“might” and “opportunity” being the key words there).