Am I missing something?
Well, first you need to completely finish the storyline (Basically defeat Darkrai) then you have to go back to Spacial Rift and battle Palkia, and then he automatically asks to join your team. Then after a few days Manaphy comes back and joins your team. Few days after that, he'll come running to Sharpedo Bluff and tells you that he discovered a place called the Marine Resort. If you have all of that done, go back to Luminous Spring and evolve your starters like you would any other Pokemon!
Source Hope this helps!
