It doesn't have to. KDE is a great example here. Out of the box, it's extremely simple to use, as well as familiar in look and feel to Windows. But if you want to - it gives you a lot of customization options. So it doesn't seem to lose out on anything due to being simplified by default.

And frankly, a lot of Unix software could use a similar approach. I know it's not that simple, but it helps the users greatly - particularly new ones, but experienced ones too. Perhaps this wave of Windows refugees will in some way lead to progress in this area.