The best counters for you are the pokemon of the 15 or so other trainers that show up if and when you ever get an EX pass. I'm not making sport, as I never have and probably never will get one of those passes, but your priorities should be to get a pass and get in a large group if you have one. It doesn't matter what you throw out there if you have a large enough group.
C/FB Mewtwo counters
What are the best counters for C/FB Mewtwo, besides Mewtwo itself? Gengar faints a but too quickly against Confusion.
PS: Just asking. I didn’t receive any EX pass.
You can set weather and boss moveset to see what will work best.
Against C/F and with no weather: Tyranitar and Houndoom still rank highly, because of the resistance to Confusion in spite of the weakness to Focus Blast. Following up are Rayquaza, Gardevoir, Kyogre, Dragonite, Latios, Latias, Scizor, Pinsir...
You can also set the level of your attackers and you dodging style. If you make no attempt at dodging Focus Blast, the these pokemon move up the list: Gengar, Lugia, Banette (surprisingly), Scyther, Gyarados, Moltres, Ho-Oh
If you have a weather forecast, you could refine the counters a bit more.
Just go with Tyranitar for all movesets. Keep it simple. My first Mewtwo raid was against C/FB in cloudy weather. Worst possible situation right? Went in with 5 others (6 people total) and my 6x Ttars. Yes they were all one-shotted. But so was everybody else's regardless of what they were using. By the time I went in with my second squad, there was only 2 of us left in the original lobby (Ttar 2x resists C) and we were so far down the damage line that I decided to go with the auto-selected team. First Pokemon in took a FB to the face before getting a single shot off. We won on my 9th Pokemon and 126 seconds remaining.
Second Mewtwo was also against FB (don't remember fast move) but at least it wasn't cloudy this time. 5 of us total and I went with 6x Tyranitars as well. Again, they were all one-shotted along with pretty much everyone else's. We won with over 100 seconds left.
Yes FB is strong and 2x super effective against Ttar but it's still top tier against Mewtwo.
I'm gonna agree with others, here, in that Tyranitar is still a great counter to Focus Blast with Crunch being a 3-bar move with an early damage window. You'll probably have to rejoin in the case.
Other good counters for Focus Blast include Shadow Ball Gardevoir (This is why I'm working on maxing one that isn't Dazzling Gleam) and Rayquaza with DT/O. I wouldn't use Dragonite for this role because its DPS just isn't quite the same given no SE and against Mewtwo this stuff makes a difference. Other good counters include Moltres/Groudon/Kyogre ONLY if they're weather-boosted, Gengar if Mewtwo knows Psycho Cut, and DT/SA Lugia if you're just looking to anchor the last slot without fainting.
I personally don't think Double Dark Gyarados stands up as well as others here due to its low DPS.