1. Those patents weren't invalidated, they expired.
2. After looking up countless places trying to define game mechanics and coming up with tons of answers (which lands "are ai systems a game mechanic" either into yes, no, or maybe); I'm going to say in the eye of people who approve patents it all falls into the same category. As long as it's a unique feature within the game, be it a mechanic, system or whatever, it can be patented. Now what counts a "unique" is debatable, though at least one rule is probably it's something no other game had done before it.
3. So that get's into Pokemon's patents. And I think Nintendo & TPC are relying on the VERY specifics of the patents (which could let other games slide):
Catching Monsters In A Throwable Ball: What other monster taming games (that are trying to not be pokeclones) do you know besides Pokemon and Palworld that specifically uses a throwable ball to catch the monster which go inside the ball and can be stored and sent out of said ball? If you describe that before Palworld most everyone would say that's something very specific to Pokemon. BTW, the other patent relating to sneaking around in an overworld is pretty much the same deal, the issue is the object being thrown being a ball.
Riding Captured Monsters: This one is more dubious, though question: was there another game before Legends: Arceus where you could quickly switch between mounts. Because that's what the patent is for, not riding a mount, but able to press a button and you instantly change to being on another mount without having to get off the previous. Note this would be different from having a mount that morphs into a different forms, it has to be mounts that are considered all different individuals and you're just instantaneously able to swap to riding the other with a button press.
Annoying nitpicks? Yes. But when two titans start to fight little things all around them are going to get trampled.
In that case, couldn't they now just change the effect of it affecting both Pokemon in a Double Battle be just something only connected to Darkrai, while if another Pokemon uses it (specifically Smeargle via using Sketch) it's only single target?
Though, now that it just can't be copied by Sketch, does that mean next time Darkrai is in the spotlight they may adjust Dark Void to being 80% again?
A man can dream though… a man can dream…