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Mine are:
5: Aggron
4: Rayquaza
3: Blaziken
2: Latios
1: Salamence
1 and 2 aren't in my team, though.
I just need Dusclops, Walrein, Gorebyss and Glalie now.
P.S. You can download a Jirachi from Pokemon Channel, apparently. Can you download any from Colosseum?
Ruby's Advantages:
You get Groudon
Latios is stronger than Latias
Sapphire's Advantages:
Kyogre has a Type advantage over Groudon
You can get Ludicolo :)
Lots more. I only have Ruby. My next-door neighbour has Sapphire. I always win against others. Then again, I have a Metagross, Blaziken, Crawdaunt, Rayquaza, Groudon and Aggron, all at Level 100 with loads of Protein, Iron and other stuff used :)