The version exclusive Pokemon in Ruby are: Seedot, Nuzleaf, Shiftry, Mawile, Zangoose, Solrock, Groudon.
Version Exclusive Pokemon in Sapphire: Lotad, Lombre, Ludiculo, Surskit, Masquarain, Sableye, Seviper, Lunatone, Kyogre.
Emerald doesn't have: Surskit, Masquarain, Meditite, Medicham, Roselia, Zangoose, Lunatone and Deoxys Normal Forme.
To be honest this was a little confusing and long to list so source: http://bulbapedia.bulbagarden.net/wiki/Game-exclusive_Pokémon#Generation_III
You defeat the Evil Team, Team Magma.
You capture Groudon.
You defeat the Evil Team, Team Aqua
You capture Kyogre
It contains the Battle Frontier.
You catch both Kyogre and Groudon and then at the end Rayquaza!
You battle against both the Teams, Aqua and Magma.
I suggest Emerald, more story, more intense battles against the evil Teams and MORE INTENSE POST-GAME BATTLES, at the Battle Frontier! From what I've heard, Battle Frontier is fun and has special rules of battling which depends on each building.