Doesn't seem like a mystery to me. We've had plenty of uncomplicated villains, and nuanced antagonists are more interesting and compelling.

Indy 5 has literal Nazis. What more do you want?

This is the best summary I could come up with:

And after that, Ridley’s Scott’s Napoleon promises to be a bloody battlefield epic in the vain of Braveheart and Gladiator, except this one examines its warlord not through his sworn enemies but via his explosive romance with Vanessa Kirby’s Empress Josephine.

Whereas four decades ago Rocky Balboa was sent out to fight Ivan Drago – a straightforward stand-in for dead-eyed Soviet power – these days his protege Adonis Creed finds himself in the ring with his old school friend, both men forced to confront their own repressed emotions in the process.

Part of it too is down to simple economics: with mid-budget films having been all but squeezed out of existence, and the threshold for box-office success now absurdly high, global takings have become pivotal to whether a movie sinks or swims.

So it’s yippee ki-yay not just for Gruber’s brand of erudite European mastermind, but also the unhinged Arab terrorist (True Lies, London Has Fallen), the icy Russian psychopath (Air Force One, GoldenEye) and the crazed Latino gangbanger (Falling Down, End of Watch).

Back in the day, it was standard practice for the bad guy to set out his stall with the theatrical murder of a civilian, before getting to the real sadism a bit later on: for Heath Ledger’s Joker this meant impaling a rival henchman with a pencil; Die Hard 2’s racketeer preferred to plough a jumbo jet full of passengers into the ground.

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There are always shifts in what is villainized in films based on current real-world concerns. I think overall people are just more aware of the nuance that things aren't as black and white as 'good guys vs bad guys'. Which I think leads to more interesting characters and stories. That being said, there's still plenty of violence and baddies (some the article mentions like Rogue AI.) They mention specific 'bad guys' of the past where they're demonizing a specific nationality... which they answer themselves why those are less:

Presumably part of it is down to a diminishing appetite for the flatly racist caricatures that occupied the attentions of Stallone, Seagal and co for so long. Part of it too is down to simple economics: with mid-budget films having been all but squeezed out of existence, and the threshold for box-office success now absurdly high, global takings have become pivotal to whether a movie sinks or swims. In other words, Hollywood isn’t just courting America any more.

Selling stuff worldwide means not pissing on those audiences.

Who is this article even for?

I do think there's an issue of political correctness at play. Top Gun had evil Ruskies, but somehow Maverick just can't name its bad guys for fear of offending someone somewhere. Part of it is greater awareness of other people in the world, part is global markets, but there's also the general sense that depicting a nation as a bad guy is gonna create an uproar no matter who is used.

Then there's the fact that a lot of people latch on to bad guys these days. Whether it's the Joker in The Dark Knight or in the eponymous Joker, social media freaks out at bad characters that can be interpreted as role models. Heck, Thanos was a genocidal maniac yet r/thanosdidnothingwrong was a thing.

Because it would be too hard not to make it look like a real baddie.

“The creatures outside looked from pig to man, and from man to pig, and from pig to man again; but already it was impossible to say which was which.”