raquaza because it can learn almost everything and its relly strong, you can find raquaza at the top of sky pillar
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Best non-legendary water pokemon would be Gyarados. Best legendary water pokemon is Kyogre.
The strongest dragon type in pokemon Emerald, Sapphire and Ruby, is the legendary pokemon Rayquaza. In terms of non-legendary pokemon, both salamance and flygon are strong dragon types.
The legendary Pokemon in Pokemon sapphire are groudon, rayquaza, Kyogre, Regice, Regirock and registeel EDIT: No you cannot unlock/get Groudon, Rayquaza, or the Regi's.
Some legendary Pokemon can't enter.
In Ruby and Sapphire, you have to fight the respective legendary before the doors open.