Fusion Tables (and KML) are rendered as image tiles by a Google server, precisely to be as fast as you observe. v3 markers are rendered in the browser, so the speed depends on the browser.
You can speed up marker rendering by setting 'clickable' false (removes DOM click targets) and 'flat' true (hides shadows). I seem to recall these double marker rendering speed.
You can also use a marker manager to cluster markers so that fewer are shown at once. They can all be seen when you zoom in.
You could also try a fast browser such as Safari or Chrome, which are both based on the (fast) WebKit rendering engine.
- Ben
Fusion Tables is fastest because Google stores and indexes the data. KML is not necessarily as fast because Google must fetch your KML - if your KML server is slow or sets poor cache headers this adds latency. But both KML and Fusion Tables render as image tiles which is faster than browser rendering.
Both KML and Fusion Tables load the infowindow content on click, so the initial download is minimal. You can do this yourself with "AJAX" techniques so that your page load is fast. But this won't speed up marker rendering, just the page load.
- Ben