Question as old as time (or 2016): Defense or Stamina?

The defense IV means you MIGHT hit a defensive breakpoint against a particular raid boss. This is highly situational and might make zero difference on the outcome of the fight.
The HP IV means you'll have a few extra HP when maxed out (or fewer, depending on rounding calculations). While 3HP is also likely inconsequential, it is a visible difference and might give you just enough bulk to fire off an extra Hydro Pump before going down. While still probably situational, it's slightly less likely to be so.

I'd go with the 2315 Kyogre personally.

Hmmm... I would say the 2315.

15/12/15. Mostly because I'm under the impression that lower defense means that while you take more damage, you also gain a bit more energy and so theoretically could get your charged move off more often.

I could be wrong about that, but that's the impression I've gotten over the past year of watching the arguments.

I prioritize defense over stamina for all the strong pokemon. Three points of defense will save you at least 1 HP on every charged attack, and possibly one on every fast attack, which on average should add up to way more than 3 HP. Unless you're getting one shotted, defense gives you more TDO than HP.

My Kyogre task force is led by 15/15/15, 15/15/13, and 15/15/12 (all a/d/s). They are righteous.

Defense over stamina...unless it is a glass cannon.

For glass canons improvement in HP IV can add a large % to it's total of HP, at lower 'break points'