Im going with Lugia. Lugia would destroy Kyogre in a heartbeat.....or maybe 3 heartbeats.
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I'm ignoring Lugia since it isn't a Water type, or that there are quite a few other Water type Legends you neglected to mention (Suicune, Phione, Palkia, Keldeo,) I'm going with Kyogre. Perma rain+Thunder is beast and would assassinate Manaphy.
I'd just like to point out though, that Lugia knows roost (which gets rid of the Thunder and Ice weaknesses) and has Multiscale (Which gives it even more longevity than it already had.) It also knows Thunder/Thunderbolt, which both Kyogre and Manaphy are weak to and thanks to Kyogre's perma rain, won't miss. Furthermore, Kyogre doesn't have the reliable recovery Lugia does (or its special defense for that matter) and no Multiscale to soften the blow.
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Kyogre, the original Drizzler, is king in this poll. Manaphy needs it, and Lugia loses to it.
Sure, Manaphy is cute, but it's not useful in battles.
So it's Lugia vs Kyogre, but I'd say Kyogre because of Drizzle and awesome movesets.
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Like everybody said Lugia isn;t water type (though he should be damnit!!! Why is he Psychic? He's the Guardian of the SEA!!) and Drizzle+100% Accurate Thunder hurts Lugia badly and Kyogre is arguably the best sweeper in Ubers... So yeah Hoenn Pride even though Lugia is awesome. and Manaphy is being used in Ubers so he isn't that bad but has nothing on the other two
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