Right now you have to use a context menu action to rearrange the extensions in that menu. That means right-clicking to get the context menu , left-click on "move up/down", rinse and repeat for how ever long it takes.
Example:
I have 25 extensions in the extensions menu (yes, I know it's a lot) and want to move a new extension all the way to the bottom because I rarely have to click the icon. That takes 50 clicks! 50!! What the hell, you guys?
Proposed solution:
Add "Customize Menu" to the extensions menu that lets you freely drag the menu entries around, similar to the "Customize Toolbar" mode.