Team Rocket could be doing both as a xanatos gambit where Giovanni benefits no matter what the outcome is. All forces that can challenge them like the rangers, police, gym leaders, pokemon league, ect. won't be able to deal with the legendary fight and a simultaneous crime wave. He'll either succeed at both objectives or only fail one while accomplishing the other.
I don't think Giovanni knew about Moltres, he just had enough information to think that there might be something powerful was living on that mountain and sent Mewtwo to find and capture whatever it was. The only reason Brock and the handful of professors he told know about the legendary birds is because he found that ancient mural carved into the wall of Empress's cave, something no one else in living memory could have seen.
It's called Operation Burning Mountain though. If Giovanni didn't know Moltres was on Mt Silver, that's a heck of a coincidence. It would also be a heck of a gamble considering all of the damage done.
If you're right about Giovanni knowing it was Moltres, that has some unfortunate implications. The only way I could see him knowing that detail is if he had access to information only those professors would know. Maybe there are undercover Team Rocket members working as lab assistants for one or more of them to steal information?
That's... Yeah, I can see that happening. Not every rocket member is in uniform 24/7, and Giovanni undoubtedly has informants everywhere. It's possible there was a leak somewhere. I wouldn't guess Oak, so perhaps Elm's place?
From what I know, Miracle Eye is a move Mewtwo can know, which lets them hit Dark Types with Psychic moves. Dark Types haven't been used against Mewtwo yet, so we don't know if they have it, but it would make sense that they do. And if they do, a Dark Type actually wouldn't be the best at resisting Psychic attacks, as Miracle Eye makes them neutral. Weirdly, the Pokémon that would be the most resistant to Mewtwos Psychic attacks would be a Psychic/Steel Type… wait...
I mean more generally Mewtwo is a legendary. Outside of a dark type legendary or the absolute best of the best non-legendary dark types I doubt he needs miracle eye.
I'm sorry, but Miracle Eye was introduced in Gen 4, not Gen 7. Also, Mewtwo was made to be the strongest Pokémon, so it could've been naturally given to it during creation. The failsafe they have is the armor, they wouldn't purposely weaken their strongest weapon unless only them can use the means of controlling it. And while I agree Dark Type moves would be effective, so would Bug Type moves. Dark Types are effective against most Psychic Types, but not a select few; I.E. Mewtwo. Since this is an Anime setting, power scaling is thrown out he window. There is not an easy solution to deal with a legendary, and Mewtwo has already done the impossible with Recovering from a Destiny Bond. Besides, I think a Metagross can learn a Dark move or two.
This doesn't actually necessarily mean that Giovanni knows about Moltres being on Mt Silver, instead it could be taken to mean that Giovanni's forces are both literally and metaphorically set the mountain on fire.
"I dunno man he doesn't sound like all that much hot shit if I can catch 'em in a Pokeball"
Oh yes, it could easily mean that as well. I suspect it's a double meaning, however. Explosions plus a fiery legendary lighting up the mountain range.
Giovanni is after something more than mere profits and rare wild pokemon, like his mother. He's using more assets than anyone will ever know of, putting a number of eggs into one basket. He's betting big, and is confident it'll pay off (and not in any monetary value). So he wants something big. Something more than what can be captured on Mt Silver. Larger than pseudo legendaries like tyranitar.
First off, Miracle Eye is learned naturally by Mewtwo. This means that, by anime logic, it could already be learned, but just isn't being used. As I said, it's a Legendary Pokémon, something that defies the limits of this world. Who said it even has a move limit? Also, don't forget that Mewtwo is a super genius, the strongest psychic. Who's to say Mewtwo hasn't just figured out how to use Miracle Eye on its own? Im not saying that Team Rocket taught it the move, just that Mewtwo seems smart enough to figure it out itself.
