I won't go into detail but you got a few of these right
Looking at my notes, I didn't have plans for who to match Darkrai and Cresellia with, so I think I'll go with your ideas and give them to Cheryl and Marley
The lake guardians ARE going together, they're so similar in my mind that I don't see the point in seperating them
Manaphy and Phione... I'm not even sure if I want to include Phione, my only plan for them is to mention that attempts to breed Manaphys have always ended in Phione hatching out, but the MC might be able to get her to lay actual Manaphy eggs