Interface consistency comes from a variety of sources, but these can roughly be summed up into into two large groups. Consistency in presentation and consistency in interaction.
Consistency in presentation
Consistency in presentation means that similar things look the same. Now, this doesn't mean that a wave file in an editor should "look" the same as a wave file in a player. But it does mean that all applications should follow similar patterns for common presentations. The basic interface in BeOS follows some conventions that are so common now that most wouldn't even think of not having them.
Here are some examples: The title bar is on top of every window, with window manipulation widgets, if relevant (zoom and close). Below the title bar is a menu bar, if one is present. Below that is possibly a toolbar/button bar. And below that is the general content, usually in a resizable pane, if applicable.
In BeOS most applications follow these patterns. Some don't, and there can be good reasons for doing so, and it's my opinion that the ability to not follow these patterns is a functionality we should keep.
Consistency in interaction
Consistency in interaction means that when you perform an operation in one application, the interaction is the same or similar to the interaction that you use to perform the same or similar operation in a different application.
Following the window example: in the BeOS window decor, you drag the lower right corner to resize the window. you double-click the title bar to minimize.
My opinion is that BeOS presents relatively strong consistency in interaction with respect to window manipulation. I withhold my opinion on the particular choices of actions. :-)
Areas for improvement
I think that GE could strengthen InterfaceConsistencyInTextEditing and InterfaceConsistencyInSelections by using a SystemKeyBindingsPreferences mechanism.
GE could also improve the InterfaceConsistencyInPreferences by using a UniversalPreferencesManagement mechanism.
The importance of opt-out
One should keep in mind that when proposing ideas for UiDiscussion that these consistency properties should be maintained, or strengthened where possible. Consistency should be the default, not the mandate though. Opt-out is important because some applications take advantage of particular metaphors which may be at odds with generally preferrable metaphors.
For example, games often define a custom interface designed to enhance the immersive experience of the game. Although generally it's a good idea in interfaces to have things that you can click on or operate on marked in some way visually (i.e. by border, highlight, underline, etc.) in a game these helpful features could act as a distraction and reduce the realism and enjoyment of the game experience.