problem

1. sbt will silently ignore unused settings.
2. Displaying warning for all unused tasks and setting will catch top level keys like clean.

scalacOptions in compile += "-X"

expectation

1. I can mark keys to be top level or secondary. (keyUsage in (ThisBuild, foo) := Usage.Secondary, probably tasks default to top level, and settings default to secondary.)
2. There's a buildLint command that warns on unused setting/task expressions with secondary keys provided by build.sbt.
3. The warning takes in account of the scope delegation rules.
4. Debug mode to display unused setting/task expressions provided by plugins, including the Defaults.

scalacOptions in compile += "-X"
^ 
[warning] Unused key: projA/*:compile::scalacOptions was not referenced by other settings/tasks.

notes

Many have brought up the idea of warning on unused. Here's previous thread on unused settings from 2011, which shows 58 unused settings.