I've been using shutter priority for casual shooting. I noticed that, when shooting in HD, variations in shutter speed become very noticeable. Higher shutter speeds (faster than 1/60s) often produce a strobe like effect. My compromise is to lock the shutter speed at 1/45s and let the camera sort out the aperture.
When I'm shooting from one location for a while and I want to get it right, I manually set the shutter speed and aperture. I use the widest aperture that works for the entire field of view that I intend to shoot.
The problem that manual solves for me is having the exposure vary as I change my shooting angle or zoom in. By going to manual, it keeps the exposure level consistent throughout the shoot.