Thoughts??

A because best IV but most importantly best moveset. D and B both have Thunder, not a strong move for Kyogre. Difference between 13 and 15 attack is negligible to superior charge move.

Unless you're drowning in stardust and rare candies and starved for charge tm's, there's no reason to power up NYTHING BUT D.

The answer here relies on a few different factors. First off, if you're low-ish on Stardust, or feel like 160 candies isn't enough, powering up D would be the way to go. It costs 31,000 dust and 28 candies to go from level 20 (non-boosted) to level 25 (boosted). This means that you could either power A, B, or C from Pokemon level 20 to 36.5, or your boosted one to Pokemon level 37.5, level and stardust permitting, and assuming you spend all your candy.
So, if you were to spend all 160 candy and oodles of stardust
to power up D to level 37.5, it would be 44CP higher than if you were to power up A to level 36.5 (3887CP vs 3843CP). At level 36.5, the difference would instead be 14CP in favor of A. If you were to spend less stardust and candy on powering these up, the difference would be even smaller.
All of that was math, and none of it was answer. For me, B and C are out of the question, as they both require a TM for Hydro Pump and will not reach the same CP as A. If you favor 15 attack, go with D. If you want the trophy of a powered up 96%, go with A. Ultimately, it is very unlikely you'll notice any actual difference in battling ability no matter which one you power up. My final suggestion would be my personal choice, A.

It depends on what you value. Some people are more practical and reason that slightly better/worse IVs will only occasionally have an impact on a battle, so they go with the option that needs the least investment. Other people just want the best, cause you can't change IVs.

If we are talking about the best, you would choose C imo. But both A & B have plenty of appeal.

The stamina IV is the least important, close enough is good enough. I like anything over 10. The attack and defence IV will occasionally determine whether you rip through a defender faster than you thought, or the defenders rips through you faster than you thought (edit: the latter not so much with current battle mechanics, given that defenders don't spam their fast move). This is because of breakpoints, and it's more important for some mons than others, depending on stats and (fast) moves.

With Kyogres current fast move being 16 base power, it's not gonna make a huge difference if falls short of a breakpoint that robs him of 1 dmg per use. But that could change. And because he can't be used for gym defense, his defensive breakpoints aren't so important either, but that could change too (also PvP). Taking 5 vs 6 dmg from a Vine Whip spamming Venasuar is a relative big deal over the duration of a battle.

Hope this makes some sense lol. The top 3 all have appeal and neither of them would be a mistake to choose, but I like C best.

Use weather boosted one.