Although I've personally never played them, all paired versions pre-Gen V are almost identical except for some pokémon and in this case the colour of the team. Personally I'd have gone for Sapphire as Kyogre > Groudon, Ludicolo > Shiftry and Lunatone > Solrock IMO.
The other version exclusives are:
Ruby: Latios, Zangoose, Mawile
Sapphire Latias, Seviper, Sableye
Seeing as you won't be affected by nostalgia like people who got them when they came out, I would say the version exclusives are the only real deciding factor.