This is EXACTLY what you need to do to evolve. Follow these in the strict order they come in.

-Defeat Primal Dialga and save the world.
-Graduate from the Guild.
-Defeat Froslass and rescue Scizor.
-Find the Manaphy Egg in Surrounded Sea.
-Defeat Gyrados and save the Phione tribe.
-Cure and release Manaphy.
-Defeat Regigigas with Team Charm.
-Clear Concealed Ruins. (i'm not sure if you have to.)
-Save Azurill from her nightmare.
-Defeat Palkia.
-Defeat Darkrai and the save the world...again.
-Recruit both Dialga and Palkia. You just might have to recruit Regigigas too, but probably not.
-Recruit Manaphy.
-Discover Marine Resort.
-And finally, go to Luminous Spring. That stubborn hole should finally let you evolve- of course, only if you've met the requirements needed for your hero and partner such as level or iq and what not.