Kyogre for sure. It's the best legendary right now and it's comparable with Mewtwo, with the former having better duel-ability and the latter having higher DPS. But yours is perfect. I would power the 88% Mewtwo next, but I would first max Kyogre.
Don't even change the moveset yet. Use Thunder to destroy other Kyogres, especially the dreaded Blizzard Kyogre!
I think I'd pick the 15-15-10 Mewtwo. It's similar to the one I have (though I have Psycho Cut as fast move) and since taking it to lvl 40 I've used it alot. Really strong Pokemon.
The other one you have has slightly better IV, but I think I'd prefer the one with 15 in attack, even if I don't think it'll make much (if any) difference at lvl 40.
Both Groudon and Kyogre are great Pokemon, but it seems like both was boosted when you caught them, so they are already at an okay level.