A eukaryotic cell nucleus is often compared to a manager, a boss, or a brain or computer, because it is "in charge" of the operations of many other things, and is at the top of a series of cause-and-effect relationships.
Working specifically with the analogy of a mall manager, we might assume that the shops in the mall are analogies for the organelles, and the manager of the mall has some authority over them and what they do (although in practice I don't think a mall manager can really tell a shop what to sell, so the analogy breaks down a bit here. It IS useful to acknowledge the limits of an analogy so that the system it describes can be more fully understood). This analogy retains the primary position of the nucleus because we can presume no one in the mall is able to tell the manager what to do, or can act with true independence beyond the manager's oversight. We might also consider the manager's access to all of the mall's security systems and other "inner workings" as an analogy for the nucleus's ability to control other cell parts and send them specific instructions.
On the other hand, it's important to remember that the nucleus isn't conscious in the way the manager is, and isn't truly capable of making independent or abstract decisions like a human.