Besides the version exclusives and the plot (Team Magma and Groudon for Ruby, Team Aqua and Kyogre for Sapphire), their intro cutscenes are slightly different. In Ruby, the player character rides a bike in some mountains with Latios, and in Sapphire, the player character rides a bike near an ocean with Latias. Some Pokemon are not technically version exclusive but are much less common in one of the versions.
Pokemon that are a lot easier to find in Ruby: Minun, Illumise, Koffing
Pokemon that are a lot easier to find in Sapphire: Plusle, Volbeat, Grimer
[source][1]
[1]:
https://bulbapedia.bulbagarden.net/wiki/Pok%C3%A9mon_Ruby_and_Sapphire_Versions
