I am using Illustrator CS6. I would like to set the pencil tool to draw all shapes as 50% opacity without having to change each shape individually after drawing. Can I do that and how?
You can not do this (though brush tool can). Sorry. You dont need to change the transparency individually though, you can select multiple shapes at a time and apply transparency to all of them in one go.
You can use brush tool instead, by double clicking it you can enable filling just like pen tool. Alternatively you can use blob brush tool.
You can also do something somewhat comparable and apply the transparency to a layer/sublayer/group by selecting it from the circle next to the name ad applying transparency. Then everything that is in that group will be transparent as a whole, so you do not get the transparency overlay between shapes.