Is there a way for Magic VLSI to become more usable? I read the tutorial, but everything just does not make sense. The layers is completly unusable because you don't know which layers is which, as they are not labeled.

The "box tool" is the magic way---this will not be going away. If you are looking for a Cadence-like environment, then you should just learn to use klayout. The GUI in magic is not implemented like klayout because magic's layout database is fundamentally different from klayout's, being based on a tesselated plane and not on a collection of objects. The GUI in magic predates not only klayout, but also Cadence, Mentor Graphics, Tanner, and every other layout editor that did not exist prior to 1985.

@User You can mouse over the layers and the layer name will appear in the window header.

I readily admit that the user interface reflects my own biases, one of which is that I want a clean interface with a maximum amount of space for the layout itself, and a minimum of window decorations. Layer names are useful if you don't know the color mappings for the technology, but once you do, they're just wasting space. Maybe a "tutorial mode" with more recognizable window decorations would be helpful to newcomers.