I've worked with several software development projects and this kind of thing frequently happens as more and more features are built into the software. The interface becomes complex frustrating and/or overwhelming for users because so many options are available, or the new functions are hidden from view and the user never has any idea they even exist.

Look at Microsoft Office and the radical change they made back in 2007. There are numerous options available - too many to show in any meaningful way. There solution was the "ribbon" design that shows you the most logical menu options based on what task you are trying to accomplish. If you're not editing a picture, you don't see those options.

I think this is a great idea for discussion as WordPress advances. Either that or (gasp) features should really be added as plugins. I already end up spending quite a bit of my dev time subtracting or hiding menu options for my users because, depending on the project, they may never have use for some of these features and the extra options just become distractions.