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I heard when the original Sapphire in Japan came out they had to take it back and tweak it because he was too powerful. Personally I like the way it looks.
It may depend who's effect activates last. For example, Kyogre comes outand starts Drizzle, and Groudon comes out and starts Drought. Kyogre would have to have Ice beam.
Kyogre has a great advantage over groudon... but you never know what surprising attacks groudon has in stored under its sleeve. Other than the 'elementally weak' factor, I think they both stand equal chances.
And I'd agree with YoMama.. about the part where whoever was activated last. ^^
Groudon is the best pokemon in game, even though Kyogre looks to be stronger. Groudon can summon strond sunshine, so solarbeam don't need charge time. After all Kyogre is a water type, so weak vs. grass. But however Kyogre can use surf as well, but since Groudon is surrounded by sun, water attacks will do half effect....i'll say groudon is better.
They've got their own strengths and counters....Kyogre's Special abilities and HP are higher in proportion to its other stats, and for Groudon Attack, Defense, and Speed tend to be the highest areas. Depending on the order in which you put them, either one could win; put a Groudon out to face a Kyogre, Drought takes effect over Drzzle and it should do a good bit of damage if it doesn't knock it out in one hit, even without Swords Dance or Bulk Up on the first turn under Drought; but put Kyogre out later instead, Groudon's screwed.
Based on types and stats, and all that stuff (XD), they're about equal.
But, being the MAGMA-Fied one, I choose Groudon!
They both look cool too, but Groudon looks just a bit cooler than Kyogre, in my opinion. But that's just me.
Also, if you look at their Shiny versions, Shiny Kyogre turns pinkish. That doesn't fit its type so well. Groudon turns a gold-ish color, which still fits Ground-type fairly well.