Kyogre power up??

There's no rush to power one up before Kyogre leaves. But if it turns out that this Kyogre is one of the best you have, then I would power it up over any other ones.

Having 40/45 IV points compared to 45 won't have a significant difference in performance over a perfect one as long as you're hitting the same quick move damage breakpoints.

No.

1. Kyogre is still around for several weeks and you could get a better one.

2. You may want to power up ice/dragons mons for Rayquaza or powerup counters for the next legendary.

3. Kyogre wont be super useful until Regirock is released.

if you're going to power up only one then probably wait, if you're going to power up a little squad then why not?