I'm not a flash user so have no real idea about all the things you can do with it. Just most of stuff I've seen seems very cartoon-like.
With VRML you have the possibility of creating a "first person shooter" game style environment (although in your case not shooting the birds!).
You can use a variety of sensors (proximity/visibility) and LOD nodes to only expose the birds, or trigger the movements, when the viewer gets to within a certain distance of them.
You could also create a "bird" PROTO which could be used for all birds but store information about plumage and movement for particular individual species of birds.
And finally, you can create quite a large environment (from wooded to aquatic to urban) and let a person wander about ... just like a 3d game.
As I said before ... it is very doable. Just how comfortable do you feel with VRML and Flash etc???
griff