eZP is chock full of names used to indicate many unrelated things at
once, and files and folders that should be placed elsewhere, too:

• override.ini and the override system for settings (could eg. rename
  the override dir in settings to 'global')

• autoload for php classes and autoload for template stuff

• fetch functions and roles-and-permission-checking functions

• icons being in /share while they should be in /design

• all std modules being in /kernel dir while they should be in /modules

• /extension dir that should be renamed /extensions

• the 'template' folder inside the 'override' one is utterly useless

• content/view view uses the node/view template, while content/view tpl
  exists (wtf???)

• the /autoload dir should be in /share/autoload

I am sure there are many other I am forgetting here, and that
experienced eZP devs suffer daily.
Please add your own requests below...