I think they both are good, but I feel that Kyogre is a bit better for the current format. It has a lot of advantages that Primal Groudon doesn't.
The first is a more reliable attack. Even though Groudon is stronger, it's harder to use. What if you run out of Stadiums? What if your opponent is running Ninetales from Primal Clash? Without the Stadiums, Primal Groudon is left with just 100, or more with Fighting Support.
On the other hand, Kyogre does 150 no matter what, moves Energy to the bench, and snipes EX's for 30. This is better because it sets up Benched Pokemon for One-Shots, and because of how useful Energy movement can be. Shifting Energy to the bench allows you to be able to power up a Type Advantage attacker for the rare instance where you are up against a Grass variant. It also helps against cards that do more damage based on Energy attached, like Mewtwo-EX and Yveltal-EX.
Kyogre also gets help from Blastoise and Archie's Trump Card (yes, I know it's called Ace In The Hole but srsly that name sucks) as a way to reliably set up Energy on a Kyogre before it Primal Reverts and gains A Growth. I know Groudon does get access to Hidden Trick, but I feel that Korrina is the better option because of how it avoids risk.
Kyogre also has a better Basic form, though not by much. The attack is better by doing more damage and recalling Energy to something else you might need to power up.