Wow... big task. I'd definitely say it's a Motion task over Final Cut.
A couple things that may help (I'm throwing a couple suggestions out there, as I don't know exactly what you need)
An Illustrator Path to Motion Shape Converter from MotionSmarts.com [
www.motionsmarts.com]
( I haven't tried it, but they do good work).
That may help a bit, but if you have 1000's of dots, maybe not. The Replicator
might help, but it's kinda doubtful, really, if you're trying to duplicate a real city and real data.
I'd say your best bet is to export a couple different files from AI. This site [
www.apple.com] says AI files will come in as a flattened file, but mentions a plugin that would help, but the maker seems to be out of business. Here's a review of Ampede LayerLink: [
www.lafcpug.org]
So here's what I'd say... make a couple layers in AI. A layer with the base map and any dots that won't need to move. Then separate layers with each grouping of dots that move together. Then export them all solo, by turning off the other tracks. Make sure to check "Create PDF Compatible File."
I hope that helps!