I'd say that both mewtwo and kyogre are set. I've maxed out two kyogre, a 93 nonlucky and 91 lucky, both same distribution aside from the 91's 14 atk, and outside of groudon ive never noticed a need for my second kyogre
Groudon, agree not much of a need, without boosting weather, machamp is a lot better against dialga and rock types (though metagross is better than both at that) and Rhyperior's good enough as a sub for agaisnt electric types, its not a hardpressing loss to not have one. Waiting for the signature move too, heard its current sets good for PvP, but not much of a reward for PvP only.
Mewtwo, you've maxed the shadow ball one and if you have a lucky shadow ball one, i'd max that in a heartbeat.
Aside from that, i'd give moltres overheat, i feel its worth the cost. I gave my Sky attacker it and its fantastic at clearing gyms and was good against those metagross raids, as well as, assuming you dont have any overheat moltres already maxed/high level, a lot cheaper than powering another moltres up
I wouldn't worry about saving 200 RC for ray right now if you are planning on raiding, in the last two weeks in lobbies with 12+ people I got around 100 rarecandy out of not using more than the daily pass and few premiums