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The algorithm for selecting an accesskey from the possible values ignores user preferences. This is wrong - user preferences should be considered before simply analysing key combinations that are assumed to be physically present.
This isn't editorial - it affects conformance of implementations by allowing them to do smarter things than the current spec restricts them to doing. In particular, the current spec directs user agents to process accesskey in a way that precludes users setting preferences.
Waiting to find out how to propose edits to the spec. The proposed edit would be a change to the algorithm described at http://www.w3.org/TR/html5/editing.html#processing-model-4 allowing the User Agent to check user preferences first, and if appropriate assign the key according to those preferences instead of the rules laid down by the spec.
Moved to github: https://github.com/w3c/html/issues/21