Main note:
I have the same question.
Side note:
Mewtwo should be your priority. Are you certain you can get an EX pass sooner rather than later? If yes, then go ahead and turn that RC into Mewtwo candy. For example, I can raid in 6 elegible gyms and always get an Ex pass.
Kyogre is a good candidate. If you arent sure about getting other Mewtwos, you should power up a good Kyogre if you find it. Last time Kyogre was available, my best was 84%. I waited to power up and spent the candies somewhere else (Rayquazas, Mewtwos, Zapdos and Groudon), and now luckily I have the opportunity to catch a better one. In fact I caught a better one already today (88%). This because after Ray, came Lugia and the Lati twins. Kyogre wasn't a priority then. Do you think you will need a Kyogre in the near future? I am not sure.
Zapdos does good against Kyogre, but this depends on how you raid. Do you raid with 20 people? If you get 1 damage ball, its gonna be hard for you to get another one just with adding a Zapdos.
If you get 0 damage balls, then in my opinion you should power him up. Especially if you dont have a Raikou available to power up instead
If anyone else could elaborate on this last part I would love to hear it because I also have another Zapdos which I could invest in.
