Which Kyogre should I max out?

I max my 100IV Kyogre but to be honest I haven't really use him.

Never used kyogre, but 15 attack is mostly preferred over everything else for that level 39 -40 breakpoint in few cases! You wont be able to hit that last break point in few scenarios. But again that difference is small! If u dont care for that little extra damage, u can go for the second one!

Since waterfall is such a powerful move, the incremental damage from the last breakpoint doesn’t matter as much (as a percent of total damage per use) as it would for moves like dragon breath or bite. I’d probably go for the higher overall IV in this case.

https://pokemongo.gamepress.gg/breakpoint-calculator#/

the immediate use for Kyogre is Regirock raids.

for Waterfall, a 15 atk Kyogre will deal 11 damage to Regirock at level 36; a 14 atk will deal the same 11 damage at level 36,5.

You can see by yourself if you want.
The bottom line: go with the second one (96% IV), if you don't mind the large amount of resources you will use. Don't go further 36,5 as it would be useless.