Board Thread:Questions and Answers/@comment-70.126.15.83-20140429132303/@comment-5275054-20140429153623

The "Train Slot" will allow you run more trains which translates to more money or materials you can bring into your station. Boost in resources.

The "3rd Rail" will allow you to have more trains arrive at the same time which means you can click through the trains a little quicker. Little time saver.

I would personally lean toward the train slot as the better investment.