Version 3.0.0.0 of s6-overlay is finally out! It's a complete rewrite from the previous versions, and should fix numerous outstanding issues, including ones related to fix-attrs not working properly with recent versions of execline, timeouts when killing services and at container shutdown, etc.
Continuous integration and pre-built tarballs are still being worked on, but you can download the source tarball and build the overlay yourself: the build system has been entirely rewritten and is now very easy to use. (Just type make.)
We really hope this version is the answer to any concern you might have had about the usability or longevity of s6-overlay. Even if your problem isn't addressed in this version, the new codebase makes maintenance easier, so we'll be able to change and fix stuff a lot quicker. This is not the end of the road, but a new beginning. ;-)