Ok, wow that was a long ass message!
Nice job, by Primal Dialga both of my pokemon were level 100 xD I train way to hard. After the storyline you should eventually get these weird dreams and stuff like that, then you will find out there are people trying to banish you because you shouldn't exist in the Pokemon World and then keep doing missions until Palkia comes while you are sleeping and takes you to the Spacial Rift, then you vs Palkia then go in his dreams and then watch a mini cutscene thing/movie and then you will vs Darkrai at some point. Also Manaphy should come back before any of that stuff happens! and she/he joins you! look for a FAQ or something. And to evolve your starters you must recruit Palkia, beat Darkrai, beat the minions and grandmaster, unlock marine resort and wallah you can evolve!
<3