Answer.They are just different variations with different Pokemon to catch in each one. Pokemon Emerald is based around Rayquaza with a slightly different storyline, whereas Ruby and Sapphire focusd on the other 2 main legendaries., Groudon for Ruby and Kyogre for Sapphire.
Also, on Emerald your characters get slightly different outfits.
You can catch Rayquaza in Sapphire and in Ruby as well.
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