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Kyogre with an Ice type move and a water type move would obviously be able to beat both of them. Though I think (I'm not that good when it comes to moves xD) Rayquaza has a better move pool? :\ And Groudon isn't really special IMO. xD
I'm going to go with Rayquaza. I've always greatly preferred him over the other two. Groudon is just plain ugly in my opinion, and I was sick of water Pokemon by the time I got Kyogre in Sapphire, so I never really liked him.
I don't like Groudon because a Surf from a Kyogre in SUNLIGHT nearly takes it down. And a Water Spout from a completely healthy Kyogre DOES take it down in sunlight most of the time.
Rayquaza.. what can I say? A level 100 Rayquaza would probably get pwned by a Lv.75 Wailord with Ice Beam.. unless it packed Thunder.
Also, the rain animation in RSE is much better than the sun one. I mean.. a ray of light that doesen't even look like one? Jeez.
Groudon. I love that pokemon for some reason. i still think it should have been a dual type fire/Ground though but I guess we had that in that generation huh?
Rayquaza. he is my favorite pokemon of emerald and back in ruby and sapphire i didnt know he was in the game until my cousin showed me him....i think Rayquaza would pwn dialga if they met.