As the game is out now for most of the world, much more info is becoming available, though I'll try and avoid story/etc spoilers if I can. Version exclusives have been updated from what we previously knew.
serebii.net/omegarubyalphasapphire/exclusives.shtmlOmega Ruby: Seedot/Nuzleaf/Shiftry, Mawile, Zangoose, Solrock, Groudon, Palkia, Throh, Tornadus, Reshiram, Skrelp/Dragalge, Ho-Oh, Latios?
New!: Kabuto/Kabutops, Shieldon/Bastiodon and Archen/Archeops fossils are exclusive to this version, but can be traded over.
New!: West Sea (Pink/Brown) Shellos/Gastrodon is exclusive to this version.
Alpha Sapphire: Lotad/Lombre/Ludicolo, Sableye, Seviper, Lunatone, Kyogre, Dialga, Sawk, Thundurus, Zekrom, Clauncher/Clawitzer, Lugia, Latias?
New!: Omanyte/Omastar, Cranidos/Rampardos and Tirtouga/Carracosta fossils are exclusive to this version, but can be traded over.
New!: East Sea (Blue/Green) Shellos/Gastrodon is exclusive to this version.
You definitely get given a Latios or Latias depending on your chosen version, though it's not known fully yet if the other one is in the same game.
Also apparently Surfing seems faster and the encounter rate while Surfing seems much lower.
Using the DexNav, as far as I can tell, any random encounter Pokemon can be found with it's Hidden Ability.