Wow, lotta Mewtwo going around. Let's slow down and take stock of Mewtwo-two because there is a lot of cross continuity going on.
First, anime-only Mewtwo-two wasn't built by Team Rocket at all, but these shmucks:
who hired a guy called Dirk to recapture it, which led to the Genesect movie prequel episode (and then the movie itself of course). They seem to have used the same process as Team Rocket's (i.e. getting Mew's DNA and cloning it). Why? Who knows. It's Syence, emphasis on the misspelling.
What Mewtwo-two isn't is a recon, the original Mewtwo is still alive and kicking somewhere. He even made a tiny reappearance in the intro for the Mega-evolution specials. And as predicted, he did turn into Mega Mewtwo X. Right here:
are both of them. No idea there they are going with this, but they didn't forget him at least.
I mean, unless there is a third Mewtwo and this cameo is entirely pointless. Which there is! But he's a mirage Mewtwo and went away with that tech. Unless there's a FOURTH! Maybe.
One point of contention is that complaints about the execution, tone, or quality of the anime are better done in the unpopular opinion thread. We might not like the canon we're given, but it's the canon we got and we can't defile that. At least here.