ADD: Vs. Seeker or rematch call via Xtransciever, the option to allow the first Pokemon in your party to walk with you (IE it could be on the options for that Pokemon, STATS, SWITCH, ITEM, WALK, CANCEL), Old and Good rods, Pokewalker compatibility, secret bases, Game Corner (an arcade for international releases).
EDIT: Some events should automatically be in-game, IE once you get the National Pokedex, Shiny Suicune, Entei and Raikou are roaming, catching them allows you to encounter Zoroark.
REMOVE: Musicals
Maybe if they ever make the third version they should take these into consideration.