Which Kyogre to power-up?

I'd personally power up the Hydro Pump one regardless of your CTM situation for the simple reason that it makes soloing Ninetails possible, almost trivial really. The 15 Attack IV is just icing on the cake. Plus you'll save a ton of stardust by ignoring that Thunder Kyogre

2

Funny, I have #'s 1 and 2. My number 2 (87%) is already Level 31 because I wanted to use Kyogre against Mewtwo (especially if it rained).

Then I waited to choose my best to power-up. I CTMed number 1 (which is my best) and started powering it up yesterday.

So, I vote both 1 and 2. Which I had 3, but I'd still be powering up Both 1 and 2. My 3rd best is an 89% 14-12-14 (level 20) with Thunder.

"not exactly swimming in CTMs"
Choose number 2. The difference in IV to the other level 25 Kyogre is marginal. Minimal resource expenditure to get to 30 and it's got 15 attack so it'll be easy to reach breakpoints in the future.

You'll eventually want to power all three up, so it doesn't matter. Start with #2, then do #1, and by then you'll maybe have some CTMs so you can get HP on 1 and 3, and then power up #3.