First up Autotune is not something you have to do it is not a "requirement". It is something you can do to get the most out of your frame. However, the default parameters (or close to them) should be fine for most people.
For those people that want to get the most out of their frame, AutoTune makes it easy. Approximately 95% of people are successful when using AutoTune without any changes to their frame. However, if you do wish to use AutoTune then you do need to achieve a basic level of construction and rigidity of your setup.
This isn't possible when carrying a large camera gimbal on vibration mounts. In this case the camera should be removed and the copter tuned on it's own. This should result in a safe tune for the copter as additional weight is added even if it is able to move around.
The remainder of the reasons Autotune won't work all fit under the "you shouldn't be flying that" category or at least the "fly at your own risk" category. If your arms are too soft for the power of your motors (I have been guilty of that one), your CG is way out, or the vibration dampening on your APM is so soft it wobbles around in flight. Then sorry, you are on your own. The Autotune feature will detect that your frame isn't up to scratch and will tell you to go fix your problems or do the tuning yourself :)
An from a personal note, as a developer I am not trying to attract people that have never flown models before (others might be, but I am talking personally). I am not trying to attract people that want to fly a 5kg Parrot AR Drone because they got the little one and wanted to go outside without getting blown away by the slightest breeze.
I want to attract experienced pilots from DJI or OpenPilot because Arducopter control is THAT good (we are there or close and I still have a few polishing ideas left), because the control system design is based on a complete physics model of the multirotor, and Autotune generates the control gains that bring them to the edge of what the copter is capable of in a single 6 to 8 minute flight. I want to make sure that the copter is easy to set up (and that setup makes sense) for an experienced pilot. This in turn makes it relatively easy for a beginner to get up to speed and have a top performing machine.
For the pilot that doesn't want to keep the CG at least close to where it is supposed to be, or make sure that all the screws on the frame are tight, or straps a 2 kW system to a $20 flimsy plastic frame, then expects the Autopilot to make up the difference. Sorry, you will be disappointed.
