I don't know why these incompatibilities exist.
I don't know anywhere near enough about javascript, jquery or drupal to work it out or fix it and I don't know how to change the documentation but there needs to be some way of warning people that there are serious incompatibilities and consequences to trying to step up to JQuery Update 6.x-2.x-dev / Jquery 1.5.
See http://drupal.org/node/1493416, http://drupal.org/node/1489344 and http://drupal.org/node/867258 for examples.
Stepping up to JQuery Update 6.x-2.x-dev / Jquery 1.5 can break major functionality (e.g. IMCE, Taxonomy Menu) in a drupal site and the incompatibility / conflict / dependencies should be documented appropriately.
Comments
Comment #1
markhalliwellDrupal 6 reached EOL (end-of-life) on February 24, 2016.