Kyogre power up question

Neither, you still have 3 weeks to raid a better Kyogre.

IF those two are still your best ones at the end, it just depends on how you value your resources. The lower level one has better IVs all around so go with that unless you're very low on dust and candy. The good thing about the L25 one is that it'll be on par with a maxed Gyarados with just a few powerups.

You can farm stardust, but not change the IV of your Kyogre. Unless you get an even better one, I would definitely go for the 96% Kyogre.

The lev 20 96% hands down.
That particular iv distribution 15a 15d 13hp at level 40 is EQUAL to the 98% with 14hp (same ps at level 40) so it's even better...
Buut...you'd better wait end of Kyogre raids, unless you really need him as a generalist attacker now (ex. you started playing recently...)

I vote for 96IV. The cost to power up from 20 to 25 only 31000 dust and 28 candies! I will power it up anyway, unless you are focusing in another Kyogre's counters. And this Kyogre can be a good counter for Blizzard and Hydropump Kyogre!

Why not both of them? I have a 2307 141215 one and still plan to up it to 30. With thunder, it is quite good to counter nonthunder kyogre, great survival against blizzard variation as well. Once the event over, i tm away the thunder for a great water attacker