Normally I'd say you are spot on, but right now you're forgetting just what Ace Giovanni has up his sleeve. The very same Ace which put Agatha in the hospital. Things might just be about to go VERY badly for everyone, not just Gio...
Mewtwo just defeated two Elite trainers on war footing at the same time and made it look easy.
Agatha is a Dark/Ghost trainer. Well, Ghost/Dark with the Dark very much secondary. She also was more experienced than Brock, though her roster and aura are both probably weaker than his.
On the other hand, Dark typing wouldn't help much against a telekinetic rock at sufficient velocity.
You're making a really great point about the difference between in-game type advantage vs in-story type advantage, but I'm afraid I can't resist the opportunity you've given me to be sarcastic.
No, but his rock-aura might make him durable enough to survive something like that. Between that and his dark typing giving him inate psychic resisitance, he might be able to actually fight Mewtwo himself. Brock wouldn't win but I think he'd be enough of a challenge to shake some of Mewtwo's preconcieved notions about humans.
I have doubts about Giovanni knowing about Moltress. I mean, there could be a separate historical record of it being in the mountain I guess, but the only one we know of is in Titan mom's lair.
He might not know that it's a moltres but there is enough information available to guess that something dangerous is in that area. Previous chapters have mentioned that wild flying types would avoid the mountain and that trainers couldn't use pokemon to fly over or climb it because their pokemon would panic halfway there and refuse to go any further. Even the rangers don't go there and Team Rocket has infiltrated the rangers enough to know why.
I feel kinda bad the Quirina the Solrock is not considered an Elite Level Pokémon yet even though Brock has had him much longer then some of his recent Elites. I wonder if he ever gets jealous of Selene the Lunatone since she gets to train with the rest of Brock's Elites and Sabrina.
What worries me is, what if he is targeting the known rare and powerful tyranitar in the range instead of the unknown legendary? This sounds like a trap for his 'biggest threats' in Lance and Brock, not an attempt to catch the legendary, it's in both their backyards, and is obviously a going in loud situation, the opposite of what Giovanni seems to favor as a method of operation. This smells like a counter to the leagues actions, and a long planned one at that. And if this is a field op with Mewtwo as the hammer to the other forces anvil, how will the undocumented legendary firebird react to another legend that smells like humans and Mew invading and razing it's territory?
They are also all fast maturity pokemon, his bug types and the unevolved Rattata can learn and grow quick, and picking up the rodents to train the Sandshrew with as training partners with the bugs as flying threats would be a great regime to toughen up fast. Add on the high loyalty of the pokes on offer, and it feels like this is a team made to push itself past it's own ever growing limits in training. He's not making a team to fight against others, he's making a team to fight against itself.
