Let's start:

Giovanni
-persian is easy, shows wealth and cunning
-ground types=underground network of Team Rocket

Archer(HGSS Rocket leader)
-Houndoom: bit of a stretch but I feel it just symbolizes the rebirth of Rocket

Maxie and Archie are straightforward

Cyrus: (some neat stuff here)
-Weavile: Ice type symbolizing Cyrus' cold soul
-Honchkrow: Flying type symbolizing the high ambition of Cyrus
-Crobat: because Cyrus has no emotion Crobat gives unreciprocated love, this furthers Cyrus' tragedy

Ghetsis:
-Hydreigon: knows Frustration, indicative of Ghetsis' pure utilitarianism of Pokemon, one of his hallmark traits

Lysandre:
-Pyroar seems to be his signature as he resembles it extremely, but
-Gyarados is his true signature, with a mega form
This I find real interesting because it's just like Lysandre's philanthropic facade while harboring an intense hate for the rest of humanity, say what you want about XY and its writing but I think it at least tried... somewhat

Lusamine:
Clefable- furthers spacial motif of Aether, not much else to say

Guzma:
-Golisopod:
weak->strong pokemon
may indicate inner weakness

Thoughts, /vp/?