This might be a terrible time for an ask like this, but I am curious about your overall stance on Mewtwo's power and intelligence.
I myself consider them to be literal demigods by virtue of both the game's Pokémon descriptions and what we see in the anime. The Pokédex claims that Alakazam has an IQ of 5000, and yet Mewtwo effortlessly wipes the floor with it. Now, I admit this is a stretch on my part, but I see this as evidence that Mewtwo can outsmart/outthink a living supercomputer. But this isn't even my main point of evidence.
Remember how Mewtwo built a literal castle and a cloning machine that outperformed the one of his creators by far in the movie? Do you think Giovanni bothered to teach Mewtwo all that? I have my doubts.
Now, where am I going with this? Well, I guess one might say that I have a bit of a hard time simply turning off my brain when the plot demands a Mewtwo to hold back with what they should be capable of, but that's due to how highly I regard Mewtwo in general. So, by this, having a way to better understand what a Mewtwo can and can't do might help me to better understand what their flaws can be, without portraying them as unrealistically weak, at least from your point of view.
As we know, Mewtwo is capable of turning the planet on its head and arguably is one of the top smartest minds in the pokemon world. He has the ability to create his own supercomputers, capable of cloning pokemon from a mere strand of dna. I dont see it as a stretch that he could outsmart one. He'd probably be able to create his own computer virus to disable it, that or just use psychic to crush it like a soda can. He covered the whole planet in a worldwide storm meant to wipe out all life, both humans and pokemon, so his mass creation of clones could take their place. The sheer magnitude of his power can literally disrupt the earth's balance, much like a lot of godlike pokemon. So seeing him as a demigod isn't entirely inaccurate.
All that being said, keep in mind that my version of Mewtwo and how I portray him may not align with how other people might view his character, and that's okay, but yeah, I know I have Jericho hold back a lot of the time with his power in my own story personally, but he doesn't do it because he's "gotten weak." The fight Jeo had with Siv when they first met, for example: He didn't go all out on her, even while in mega form. He was rightfully angry and fought to protect Lakota, but he really didn't want to hurt Siv. He was also internally conflicted since they were actually bonding and getting along well prior to Lakota showing up, but Siv forced his hand. Even then, the worst he did was grind her face into the side of a mountain (which to us really would’ve fucked a human up, but to a mewtwo, it hardly did anything). He was choosing to be the bigger man in that situation and did his best not to escalate it more than what the fight had already turned into, hoping that Siv would calm down. Also, his battle with the pack of houndooms. He really could've done much worse to them, but he chose not to take it that far, regardless of how pissed off he was.
He didn't have to go full god mode to get the message across; A mewtwo isn't a pokemon to be messed with, and they don't need to show off all their power to prove that. Jericho has instilled fear in the hearts of many with his power, but that's not the kind of reputation he wants. He chooses to use restraint in certain situations. Holding back isn't always weakness or a flaw. It can be viewed as being wise, responsible, and self-aware. Knowing the amount of destruction you have the ability to cause and choosing not to act upon it is one of the biggest strengths any character can have, regardless of what a story plot demands or doesn't.
Jericho is not as ruthless or reckless with his power as he used to be, nor as he could be now...appreciate that
