Which do you prefer?
Psycho Cut is faster and it can be more useful to Psychic type enemies like Mewtwo itself, while Confusion clearly does more damage.
Confusion- just because if I recall correctly if you opt for PC the neutral DPS drops to a level that is only 'just as good' as Dragonite.
There is no reason to use mewtwo against mewtwo when ttar is clearly the better option, except against focus blast. Realistically the only mainstream opponent that would call for a PC/SB mewtwo is FB Alakazam, so weigh in your interest in that.
I also opted for Confusion simply because the overall damage output far surpasses Psycho Cut. That being said, it's much easier to dodge with Psycho Cut, so it has some advantages in that respect (the higher DPS of Confusion means little if you miss dodges and faint sooner, thus firing off fewer Shadow Balls).
Presumably for use against another Mewtwo raid? You want the better EPS and dodging of Psycho Cut/Shadow Ball. Most of your damage will come from Shadow Ball and you want to use that as much as possible.
If we are talking just regular gym fights, I think Confusion/Focus Blast is the preferred moveset because of all the normal-type defenders. My Mewtwo started with Psycho Cut/Focus Blast. That is a bit too reliant on the 100-energy charge move for damage. Confusion is lower EPS and not as good for dodging, but the higher DPS works better when you don't want to waste Focus Blast on a weaker defender.
Interesting approach. I have two Mewtwos, one with C/SB, and one with PC/FB. I use the C/SB one as a generalist and raid attacker, and the PC/FB one mostly for gym attacking, particularly against the fat normal types. I prefer PC for gym battles, because I usually have the time to dodge all I want, and can focus on conserving resources and avoiding having to switch attackers any more than necessary.
For raids, where the importance of dodging is greatly diminished, I prefer the high DPS of confusion. I don't dispute that PC may be better against Alakazam and Mewtwo bosses, but confusion is better against Gengar and Machamp bosses, and also as a hard-hitting generalist for gyms.
Because you want a Mewtwo with Shadow Ball, that leaves two options: Generalist/Psychic specialist or Ghost specialist.
Mewtwo's premier role is as a generalist. With Confusion/Shadow Ball, put it in any raid team and it will often keep up with specialized counters. In some instances, it will even exceed them, as seen in pre-Groudon Raikou raids. Confusion/Shadow Ball also allows it to further destroy Pokemon weak to Psychic, which is seen in many raid bosses such as Machamp and Gengar.
Psycho-Cut/Shadow Ball is better suited for countering Psychic types. This helps it to stand up to Alakazam and Mewtwo, but it at best keeps pace with Bite/Crunch Tyranitar unless the charged move is Focus Blast. It also helps with dodging which is good for Gengar's high attack and super-effectiveness, as well as Machamp's Steel movesets.
Overall, Confusion gives Mewtwo a lot more options. I'm definitely going to max a Psycho Cut/Shadow Ball Mewtwo eventually, but this is only well after I've maxed my Confusion/Shadow Ball Mewtwo (And perhaps one with Confusion/Focus Blast too. Psycho Cut/Focus Blast isn't worth mentioning, as are any other movesets).
