RUBY
Based off Groudon
Team Magma
Magma wants Groudon for it's powers off evarporation and to reshape the earth
Red

SAPPHIRE
Based off Kyorge
Team Aqua
Aqua wants Kyorge for it's power to flood the earth
Blue

EMERALD
Based off Rekkuza
Team Aero
Aero wants Rekkuza for it's control over air, temparature, and weather
Green

In this game, you can pick a new boy/girl, and Yuuki and Haruka are both your rivals. You are a young b/g who lives in Mishiro Town. Prof. Odamaki asks you to deliver something to his assitant near Kotoki City while he takes a stroll. After you deliver the item, you head back and see the Prof. being attacked by a Pochena. You grab one of his Poke'balls and send out a Poke'mon to defeat it, when Yuuki and Haruka arrive at the last minute. You discover that one of them is Odamaki's child and the other is Senri's child. Odamaki then takes all 3 of the kids to his lab and decides to give the 3 each a Poke'mon. (From this point on, lets just say Haruka is Odamaki's daughter and Yuuki is Senri's son). One to Haruka because she's his daughter, one to Yuuki because he is the son of a gym leader, and one to you for doing the favor and saving his life. Whatever Poke'mon you pick, the child of Odamaki will have the weaker type and the child of Senri will have the stronger type.

You start your adventure and have a quick run in with a member of Team Magma at Kotoki City. Later, you run into a member of Team Aqua at Touka City. These two gangs will harrass you through the game, but it's Team Aero who is your true gang enemy, who want Rekkuza for the power to control wind and air.

Team Magma commonly use:
Pochena, Donmeru, Slugma

Team Aqua commonly use:
Pochena, Kibania, Magikarp

Team Aero commonly use:
Pochena, Knuckler, Doduo, Zubat

You will be able to catch either Groudon and Rekkuza or Kyorge and Rekkuza

Abusoru, Zanguusu, Runatoon, Rabukasu, and Kokodora are unobtainable in Emerald

You will see Rekkuza in the wild before trying to catch it on Illusion Tower

Yuuki's Team
Treecko/Sabonea
Torchic/Kootasu
Mudkip/Kibania
Kecleon

Haruka's Team
Treecko/Kinokoko
Torchic/Donmeru
Mudkip/Wailmer
Oosubame

These are some ideas. Will update.