Thesuzerain has told us that there are three faction-like "clubs". Each club contains its own side missions and includes a legendary that is specific to their quest line.
Rangers take care of Pokémon and wildlife. The Rangers club house is in Kivu town .
The ranger quests lead to Manaphy and therefore Phione.
Law enforcement. Their clubhouse is located in Fianga City.
This quest line leads to Mewtwo (and his Psychic/Dark form) and is required to catch Mew as well.
"Evil" Club: Cipher or Magma/AquaEdit
During the 2nd region you are asked to join either Team Magma/Aqua (the "good" guys) or Team Cipher (the bad guys).
Note: The team you join determines what megastone you receive for Charizard.