-Kyogre's trait only helps itself and other Water/Electric pokemon on the the team. You already have Kyogre as a water pokemon, why would you want to overload your team with more of them? You are asking for your whole team to be easily countered by Blissey. Just for the reference, a Blissey with Special Defense can take on Kyogre. Defense EVs are too risky to sacrifice in the uber metagame... Also, Shedinja ****s up Kyogre something awful. Hope you have Spikes, and Skarmory/Cloyster won't last in the uber metagame.
In comparison, Groudon's trait helps itself and any Grass or Fire pokemon you have. If you are afraid of Sunnybeamers, use Rayquaza. Ground, Grass and Fire surely is a more diverse team than EXCESSIVE Water and Electric. Just a side note, Metagross with a Sunny Day up SCREWS stuff in the ***. The common counter for Metagross is either a Water pokemon or Skarmory... Sunny Day lets you release a STAB HP Fire to Skarmory, and Water pokemon can't hit you nearly as hard with Sunny Day up.
-Kyogre only has Calm Mind, Groudon has Swords Dance. Kyogre only hurts when the Rain is out... Rain or Shine, a Swords Danced Groudon Earthquake WILL **** you up.
I love smogon