Well.. I count myself as one of the manual focus crowd, as well as anyone who uses anything but a point & shoot camera. As you said, it's the focus point gets you. The "bird in flight" photo you describe is a great example. Are you managing to keep the bird on the auto-focus point (or the majority of points for multipoint focus)? While you're tracking it? Including when you press the shutter?
I've seen a lot of photos like that, and they do a wonderful job of some very pretty well focused cloud photos, with a blurry spot in the foreground.
Most people will mangle the bird in flight on an auto camera because the shutter speed was too long and the photographer's tracking wasn't perfect (and the bird did something silly like flap it's wings). Most of the point and shoot I've used refocus when you actually shoot, so there's an extra second while it adjusts, while the bird disappears from your view. Most of those either focus on the clouds, some tree on the horizon, or tall grass in the foreground.
Manual focus, you can set the focus with the bird on the ground. Your effective ISO (for most decent DSLR) and shutter speed were already set. If you use manual focus cameras, you intuitively readjust while you're shooting, so a change in distance isn't a big deal.
This camera actually looks pretty cool, since it will compensate for that. "damned close" becomes "perfect +- a good bit". Did I want the birds wingtip or his eye to be focused? I can look at the options later. :)
I'm annoyed more than anything, when I only have a point & shoot (like at an amusement park, or other places that I don't want to carry gear), and the perfectly framed snapshot (heh) ends up focusing on the wrong thing, is hopelessly blurred, or just took too long to auto-adjust before actually taking the shot.
Like, if you're taking a photo of your kids on a roller coaster. You snap when they come into view. It adjusts and takes the photo either as a blur of the last car, or a perfectly focused and exposed shot of the tracks. "Ya kids, I saw you rolling down *those* tracks!".
I'll admit, sometimes I do get lazy, and leave everything on auto. When I want the good picture, I switch to manual.
In your "bird in flight" example, sure, if the camera is set to all auto, I'll track and shoot, and hope it comes out. If I see the bird getting ready to fly, I'll take the time to get the good shot.