> The multi-window interface. I know you can change this, but there's no good reason for not being the default since the beginning.

There is. It has bugs.

> God help you if you close the layers window and don't know how to bring it back.

You mean god help those people who don't see the Window menu in the menu bar?

> Overlap in functions between different tools. For instance, the perspective tool and the cage tool.

There is no overlap between those two whatsoever. None. Nada. Zilch.

> doubt anyone knows the difference between "screen", "window", and "deactivated".

Everyone who understands English?