You have the right idea by using regions, but it sounds like you want
to have more regions, each one with fewer polygons. I'm guessing
(hard to say without seeing your KML) that you are putting all your
polygons into a single region, which would mean they all get loaded/
parsed as soon as that region comes into view, which could cause the
bottleneck. If you're still having troubles, please post a link to
your KML.
Cheers,
-Josh