Finally a milli. What now?
Sorry for the humblebrag, but I worked hard for this! So now I guess it is time to go on a spending spree. Or at least spend some. Here are my current best stardust candidates:
Pinsir 93% att15 L30 to L30,5. This seems like a no-brainer since it reaches the damage breakpoint against mewtwo here. Scizor 93% att15 L30 to L31,5. A bit more expensive than the Pinsir, but likewise not too expensive. Alakazam 100% PC/FS L20 to L30. This used to be a no-brainer but with MewTwo about to enter the scene it might not be worth it. Still it is a 100% and it is a huge attacker, so I'll probably do it. Dragonite 91% att15 DT/Hu.L20 to L30. I have only one L30 Dragonite, which also has DT/Hu. I can't seem to get Outrage (spent 6 charge TM's in vain trying to get it). Not really sure if this is worth it since Dragonite raids MIGHT be just around the corner. Zapdos 91% att15 CB/TS. This is my best legendary. Have caught 20-25 legendaries in total, but still not one higher than 91%. The only reason I haven't already powered it up is that there is still time to possibly catch a better one. Moltres 89%. My best Moltres. Will power up if I don't catch a better one. Lugia 89%. My best Lugia. Will power up if I don't catch a better one. Articuno 82%. My best Articuno. Will power up if I don't catch a better one. Tyranitar: I'm still looking for a B/C Tyranitar. Have three L30 B/SE ones, but would rather power up a fourth B/C than TM any of my current ones. Don't currently have a really good L20 Tyranitar though and none with Crunch. Last 5 or 6 Tyranitar raids I failed to catch it. Driving me nuts. But I need to have dust for when it hopefully happens.If I do all of those, that's more than half my milli. Worth it?

Answers
Try do some Tyranitar raids. That is, generally, your best shot by far for Mewtwo with Physic, Hyper Beam or Shadow Ball.
If it has Focus Blast you could try Dragonite. Or, even better, level up a Shadow Ball Mewtwo with that star dust once you manage to capture one.
I guess you already read it, but just in case:
https://pokemongo.gamepress.gg/countering-mewtwo-and-mewtwos-place-meta
Yeah, currently I rarely go further than L30. At this stage of playing I feel it is more important to have a well rounded team of L30 mon rather than a few maxed out supermons. Before the gym rework I was spending all my dust on defenders, so I had a huge lack of quality attackers.
Having said that: A great IV Mewtwo will get maxed no question.
Im acctually in the similar situation Albeit less dust.
As follows is just my opinion and more experienced players can probably help you more.
I Changed one of dragonites hurricane to outrage. Don't think it makes any larger impact. Im taking dragonite into my team as a semi anchor in case of focus blast, the bulk of my attack will tyranitar and the bugs do.
Currently dust hunting; Tyranitar and pinsir. Sticking with SE. Given up on double dark + SE will be useful against ho-oh. So imo;
Power up pinsir and scizor; good for future.
Don't get hung up on tyranitar with crunch.
Don't get hung up on dragonite with outrage, your teams main attack will be done others. Probably won't use dragonite if you are in a highly active area with many players.