The pen tool certainly does have its uses (which is why it wasn't removed completely) but unless you are either very familiar with how bezier paths work or have used a similar tool in another application then it takes quite a lot of getting used to before you can use it well. The shape editor and freehand tool seem to be much easier for new users to get to grips with so the decision was taken to remove the pen tool from the standard toolbar setup to avoid confusion.

Gerry