There's Manual with Auto ISO, which does almost the same as Aperture/Shutter priority, but lets you select _both_, and the camera chooses an ISO. Or you can specify the ISO as well.
Nikon, Sony, and Canon all have _excellent_ metering systems, but there are two main reasons I sometimes ignore them and go full-manual:
1. In tricky lighting environments, where a face is in shadow, but another is not, and zone or spot metering is causing the camera to meter for the wrong part of the frame. Think dimly-lit weddings, PJ scenarios in night scenes...
2. When you're shooting something with a uniformly-lit area (e.g. stage, sanctuary, podium area) and you can lock in the exposure so you don't accidentally get a few frames underexposed because the meter was looking at the black curtain and not the bright face you focused on.
It's not often, but I'd say I switch to M at least once on almost every on-location shoot, whether natural or artificial light.