Is it possible to add a Polygon layer to a google map v3 without using fusion tables
Solution 1:
The Google Maps API provides a pretty straightforward method to draw polygons.
Basic Example:
var polygon = new google.maps.Polygon({
map: your_google_map_instance,
paths: array_of_latlng_points,
fillColor: "#336699",
fillOpacity: .5,
})
EDIT: For this approach, you would need to parse your KML files (sorry, must've missed that when I first read it). You can import the KML files to a KML layer
Solution 2:
You can overlay Polygons using KmlLayer, FusionTablesLayer (as you know), or native google.maps.Polygon objects.
KmlLayer and FusionTablesLayer render them as tiles, so for lots of Polygons (if you only need click events) will be more efficient. There are limitations on the number of KmlLayers that can be displayed on the map at one time and on FusionTablesLayer (but those don't seem to be causing you problems).
There are also third party parsers available for KML (geoxml3, geoxml-v3) which will take your KML and render it as native google.maps.Polygon objects. For lots of Polygons, this will be less efficient than tile based rendering, but it does allow mouseover/mouseout, and changing the properties of the Polygons dynamically.
Solution 3:
You could also try data layers what have lots of events so you can display tooltips, info window, status text on various mouse events. See samples in documentation: https://developers.google.com/maps/documentation/javascript/datalayer
If you have many polygons (where the actual value of many depends on multiple factors, can be anywhere between 100 and 1,000) the best is to use a built in layer type. The fastest are the ones rendered on server, e.g. kml layer because this doesn't create hundreds of DOM elements in browser but still exposes click events so infoboxes can be displayed for each item.
In the worst case you can implement your own rendering with an image map, obviously by using an existing library like mapnik. https://developers.google.com/maps/documentation/javascript/maptypes#ImageMapTypes