A hat riding a mage?!
Quote from Greenalink:
You can only get the master ball at the last part of the game, also some shadow PKMN have a limited appearance from NPCs (Entei only appears twice and if you fail to capture it, it won't come back).
The gerbils are re-catchable in Deep Colosseum (that's after beating the game), since the finals there have you fight the admins. Source, section 6-h.
You cannot completely miss any pokemon in the game, or in XD for that matter.
I'm looking forward to hearing more about the route for this run.