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i just dont get the hub-bub over this issue,maybe I suck ...lol
Think of Auto-ISO in M as basically a combination of A and S modes, combined.
Supposed one is shooting sports and you want to simultaneously ensure
1) Adequate DOF so you want to stay stopped down some and
2) Adequate SS to freeze action and
3) The lighting/metering is non-constant.
Using only A mode, the "normal" Auto-ISO logic may not give you a fast-enough SS to be helpful (let's say it calculates 1/Focal length and you're shooting with a 300 2.8, but you want 1/500s)
Using only S mode, the camera is going to open up the aperture before it starts raising ISO in auto-ISO, but if you wanted to stay stopped down for any reason (maybe you're shooting a dog competition and you want more DOF than what 300mm 2.8 gives) then you're screwed in this mode too.
Auto-ISO in "M" solves all of this...same with Exposure compensation in "M" mode.
Let's say in this same doggy competition, you're shooting a variety of breeds, some are snow-white and then you turn and start shooting a chocolate lab. Auto-ISO in "M", combined with exposure compensation, is an extremely elegant solution.