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1) The pokemon you can catch. With Sapphire, you'd catch only Lotad compared to Ruby's Seedot, Lunatone compared to Ruby's Solrock, Seviper compared to Ruby's Zangoose, Kyogre compared to Ruby's Groudon, Sableye compared to Ruby's Mawile, and a few more. For the rest, check out serebii.net
2) The teams you'll face. Ruby gets Team Magma, while Sapphire gets Aqua.
If you want more info, then check out serebii.net.
My personal prefernece is sapphire because you can cacth Kyorge who is a water type my favourite type. But both are good games and relatively the same.Or you can wait till emerald comes out and get the best of both worlds
a major choice depends on your starter, and in what version. If Sapphire is your choice, then a lot of enemies you encounter will be from team Aqua, who use water Pokemon, and Treecko will wipe them out. However, pick Ruby and get team Magma as the opposing force, as they mainly use fire types, Mudkip can wash them away. Or pick Torchic, and have a mixture of both.
Alright, so Ruby has team magma, but I hate mudkip, it has groudon which looks good to me because he has fire blast and solarbeam, but saphire you can get more water pokemon and I am going to choose torchick anyway to get blaziken so I won't really need groudon...