Which Mewtwo to power up?

The 91% one, he will last a bit longer and will have at the end a higuer CP

I'd do the 89%. Better attack and defense, and the ultimate difference in Stamina is like 3 HP, if that.

Power up both, Pokebattler recommends my Mewtwo in the Top 6 (usually Top3) for almost everything (Confusion, Shadowball)
Plus, you have the Opportunity to make Mewtwo both, your best Raid Generalist AND your best Gym Attacker by giving one Confusion + Shadowball and the other Psycho Cut + Focusblast
I would love to have another Mewtu, even if it had "only" 80%
91% Confusion
89% Psycho cut due to higher Attack Stat in case for breakpoints

Instead of starting another thread i'll just jump on this one.
2250 91% 13 attack (15 d 13 h)
2247 89% 15 attack (14 d 11 h)

Also you can settle an arguement between my kids. both have level 30 Mewtwos.
3371 89% but 15 attack (13 hp 12 d)
3386 93% but 14-14-14

Whichever I power up will end up in between them at 3375 or 3372

I think it would depend upon how many candies you currently have, what movesets (and if you have TM's to spare)? Personally, if I only had the limited resources to pick one (with optimal moveset), I'd go with your 89%. Unless your ultimate goal is soloing content, either one would be fine really.