Auto ISO in Manual exposure setting mode, with the right settings pre-established works great in the "new" Nikons. In the new Nikons, Auto ISO has a high degree of user-adjustments that are pre-programmed into the memory bank, and exposure compensation works perfectly.
I like Auto ISO in situations where there can be BIG, major shifts in lighting levels, such as shadow/sunlight transitions, or where you want to be able to capture a subject that will move from a bright area, to a much darker area in a VERY SHORT amount of time: think of Coastalconn's osprey dive sequences, for a good example.
I'll never forget the first day I used Auto ISO, it was a portrait shoot right on the beach at the Oregon coast, steady winds of about 15-20 MPH, with occasional gusts up to 30 mph. I had the 200 VR and the 80-200/2.8 AFS on almost all day. The issue though was needing a FAST speed of 1/1600 to keep the wind from spoiling shots, to allow the subject to move and romp, at an f/stop of f/5.6 for the right background/depth of field and best image quality from the 80-200. And I wanted the ability to shoot toward the sun, backlighted, and side-lighted, or (later in the afternoon) front-lighted, using the sun as a crisp main light.
Auto ISO was a MAJOR factor in making it easy to just look thru the viewfinder, and work on composing, tracking, and getting the right timing.
Auto ISO in the earlier D2x Nikon was USELESS, since the sensor was only good from ISO 100 to 320; on the newer Nikons the usable ISO range is much better. It's my understanding also that other brands have significantly different, less-adjustable AUTO ISO methods.
There are many times when what you want is a specific shutter speed and a specific,exact f/stop. This is where Auto ISO in Manual exposure control mode has been the best for me. When I want to be able to set a certain, exact, specific exposure that has a real significance, and then let the ISO be moved to achieve the right level of sensor gain to get what I envision.
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I do not use AUTO ISO with flash, since most of my flash is shot at low to medium ISO values, and the majority of the exposure is from flash illumination. I shoot flash in M mode, always, figure out the flash power, and I set the shutter speed to control background brightness if there is an ambient light source.