ACHIEVEMENTS SYSTEM:
I suggest an achievements system. For instance: once captured all water pokemon from Kanto Region, you would receive a badge or another symbol. If a player catches all pokemon, get all items, etc... or simply reaches 100% of the achievement system, a public symbol could make visible outside to other players.
DAILY LOGIN BONUS:
Common in others MMORPG.
FLY:
New and nonofficial points of landing in the maps. For instance: fly directly to specific points of Hoenn Sea, or Sevii Islands, etc. Also "Fly Ocarina" do possible to fly to others regions without ship necessity.
PERIODIC CHALLENGES:
Weekly, Biweekly or Monthly.
POKE RIDE:
:) please...