The Version 1.4 update, released to address several gameplay bugs and enhance connectivity, is the definitive version of the game.
If you have your base game file, you will often find the update CIA available separately. Here is how to apply it generally: pokemon omega ruby update cia decrypted
Also, remember that using a decrypted update to play a ROM you do not own a physical or digital copy of is piracy. Support the franchise! (Though, admittedly, Nintendo no longer sells the 3DS eShop updates). The Version 1