While the patch notes are vague and non-specific, fans have discovered some of the changes. This update does not provide support for the Generation II Virtual Console games (Pokémon Gold and Silver will be released on 3DS Virtual Console on September 22), but it does update the way it converts Pokémon from Generation I so that they are not inconsistent with how they would be in Generation II.
Specifically, this update makes a Pokémon's gender when transported be based on its IVs (in Generation I) rather than random. It also correctly implements the method for determining whether a Pokémon is Shiny based on its IVs in Generation I; prior to this update, the roles of Attack and Defense were reversed (resulting in the same odds). These changes mean that Pokémon traded to Generation II will have the same gender and Shiny status as when they are transported to Pokémon Bank.
“Adjustments have been made to make for a more pleasant gaming experience.”