Insufficient distinction between running and favourite applications in Launcher
Unity first brought with it the 'launcher' which was designed to display both running and favourite apps thereby acting as a launcher AND a window switcher. The current implementation of the 'launcher' works well as a launcher but requires much more thought from the user when it comes to switching windows, this (for me at least) is Unity's biggest stumbling block when it comes to multi-tasking.
The problem is that it is difficult for the user to, at a glance, distinguish between running and favourite apps as they are often dispersed amongst each other. This means that when switching windows the user must first search through the list of (many) apps to see which are running, then can think which one was it that they wanted to switch to.
Although this might not seemed like much of a difference it requires a lot more thought process from the user compared to if they were presented with the running apps and favourite apps "separately".
(I find that usability is greatly increased in Unity if i do not pin any apps to the launcher and only use it for switching apps. Give it a go.)