Will we have the chance to face some of the gen3 legendaries again before gen4?

Nobody knows.

Kyogre returned for two weeks in June.

We already had the second return of Kyogre. I’m sure Groudon and Rayquaza will come soon, maybe alongside another legendary for their shiny version. However I’m sure they will be a research breakthrough at some point.

Kyogre already returned for two weeks in June, so it'll most likely be a while before he's available in raids again. However, I'm sure in the next few research breakthroughs he'll be in one. As for rayquaza and groudon, I've also been waiting a while for them to return. I think they'll be in raids either in November/December.

Further, by finishing the beasts this month, we will either get Lugia, Ho-Oh or Mewtwo as Field Research Breakthroughs, or we'll start on the Gen3 legendaries. I'd love three months of catching 4-5 Kyogre, Groudon and Rayquaza at 6 candy a pop, even if they are only level 15. It will also allow players without a big community to do raids with to get these powerful pokemon and start using them.

So if you don't have the Weather Trio, don't despair. They are coming, one way or another.

When it comes to Legendary raid bosses, I'm cool with it if Giratina is next, I'm cool with it if Groudon/Rayquaza or both are next, or even a Gen4 surprise. But if we get another two weeks of a substandard legendary (Lati@s, Ho-Oh or Lugia), I'll be kind of annoyed, and go back to raiding Kirlia, Piloswine, and so forth, like I was during the end of the Regis.

We'll know by 10/23 what's next (announcement probably a day or two before that). Hang in there.

Kyogre has been in rotation 3 times I believe, the other two only twice. It’s possible Groudon and Rayquaza return in some form but Kyogre I’m unsure.