I always like a nice Flash menu. I think it goes fine with the rest of the site, and 'cause the opening animation is on a mouseover, it isn't really in the way. I'd totally keep it. Just one thing... the gear animation... it looks like you did a bitmap trace or something... I'd suggest tracing over the bitmap with vectors by hand, and then replacing it in the tween. And yes, the into-page is annoying. Otherwise a very clean layout. Nice looking work.
If you want to see what too much animation is, see this:
http://robodox.tripod.com It's a layout I made a while back that the team never tried to use for the official website. I need to make one for the official site one of these days...