The Extra Step
Beware of the extra step. If it is part of a procedure that the user carries out within a software application, chances are that it is an action that will be repeated many times over.
When creating diagrams, a common action is to center a connecting line with the object it connects to. In Freehand, this could be accomplished in three clicks: 1 each to select the objects to be aligned, and one to press the align button. The default behavior in Freehand dictates that if one object is narrower than the other and is within the bounds of the wider object, it will center to the current position of the wider object without the wider object moving. 99.9% of the time, this is the desired behavior.
In Illustrator, this is not the default behavior. Instead, both objects will move an equal amount of distance toward each other to center on the space between their previous positions. To achieve the aforementioned behavior, you must select an option to center on a key selected object from a menu. Then, if the wider object isn’t already selected as the “key”, you must click on the object that you want to be the key. This takes twice as many clicks to accomplish in Illustrator, and I’ll likely do it over a hundred times while creating a diagram.

