Kyogre or Rayquaza?

Have you already powered up one (or more) of each? I'd start with the Kyogre, but eventually cover both; water-type offense is generally more useful at present than flying-type offense, both in gyms and in raids. And you'll get enough TMs with time to dragoon your Ray if you wish.

I use my maxed out Ray all the time. Kyorge is great but not as versatile. Both have alternatives (Dragonite and Gyardos) who are almost as good.

Go for Rayquaza...
But you got to change his move with 2x Dragons... esp dealing with the current T5 Boss... Btw 2x Flying in not that bad...
Good Luck!!!

Rayquaza. It has potential for the 2 man latios if you're into that sort of thing.

The only boss where you 'needed' kyogre is claydol but it's not there anymore.

Kyogre is more then a little better gyardos and as it stands will remain the most powerfull water mon.
Raquaza is currently the best dragon type but the margin isn't as great over dragonite but you ll get good use from it for the next 2 months which should let you reclaim the resources. And when it is exceeded by future dragon types then you'll tm it to remain the best flying type ( for what that's worth).
Id go rayquaza first then save for kyogre before the regis are out.