Let's see...here are my hypotheses:
I think Pidgeotto and Pidgeot will move in a manner similar to its Emerald animation. Or, it might flutter in place dramatically while hovering over the ground, possibly perching at some point?
Weedle will squirm, look around with insecurity, or rear its feeble stinger towards the player.
Rattata will scurry above, while Raticate will bare its fangs and claws towards the player, occasionally standing up on its hind legs to do so.
Spearow will have an animation similar to Emerald, while Fearow will peck in the air as it darts its neck occasionally.
Sandshrew will curl up in a ball and uncurl; and Sandlash giving foes a few swipes at the air as a testament to its fighting spirit.
Diglett literally "pops up" once in a while, while 2 of Dugtrio's heads scan the terrain to ensure of no disasters...
Groudon, Kyogre, and Rayquaza will have their insignias glowing periodically, similar to the pattern of the electric bulbs of Chinchou and Lantern...
Many more ideas to follow later. ;)