If you know other people who have one version but not the other, you can get the one they dont have, if you know poeple who have both then get the one you think looks cooler. Same goes for if you dont know anybody with either. I personally prefer Saphire and Kyogre.
Pokemon exclusives
Ruby-Saphire-Advantage
Seedot-Lotad-Saphire
Solrock-Lunatone-Tie
Mawhile-Sableye-Saphire (I am partrial to Sableye)
Zangoose-Seviper-Ruby
Latios-Latias-Ruby
Groudon-Kyogre-Saphire
I believe that is all the exclusives, some are alot harder to catch in one version or the other, but not impossible. Whichever you choose, it will be loads of fun