Mewtwo Y is generally much better than X, however it depends on your team.
It has a better speed tier than both regular Mewtwo and Mewtwo X at 416, which means you're not having a speed-tie with Mega Gengar (394 Spe). Mewtwo Y's STAB and coverage options are all more spammable. It is not stuck with Zen Headbutt like MMX nor forced to run a mixed set to be viable, and Fire Blast + Ice Beam coverage pretty much breaks everything.
While it is also a lot more vulnerable to priority from Yveltal, Marshadow, Arceus, etc. Mewtwo X despite looking to have a better Arceus match-up faces a lot of competition from Ultra Necrozma as a Psychic-type and Marshadow for a Fighting-type as they don't take up a Mega slot and are very versatile regardless. Mega Lucario also has a good priority in Bullet Punch, and resisting both Sucker Punch and Extreme Speed better along with better immediate firepower just makes it preferred over Mega Mewtwo X. Due to all of these reasons, it's only ranked C+ in the viability rankings. Mewtwo Y meanwhile, boasts a better position at A-.
Source
Overall, Mewtwo Y is an excellent special attacker with one of the best speed tiers (only behind Deoxys-A, M-Aerodactyl and Pheromosa) with great coverage options with access to Calm Mind and arguably the best special Psychic-type move: Psystrike. Mewtwo X, on the other hand faces a lot of questions on its viability compared to using Ultra-Necrozma, Marshadow, M-Lucario, etc. and is rather niche. The choice may change upon your team, but Y is easier to fit.
Hope this helps :)
