Developing a course that compares old and new features

For its longer-term usefulness, I agree that the training should only focus on the current process. As Tom pointed out, new users don't need to know how things used to be. That excess info just increases their cognitive load, confusion, and consternation. 

However, depending on the type of changes, it might be useful to provide a "delta" course that explains the changes--ideally in a way that motivates long-term users to adapt. Perhaps present a scenario that highlights the benefits of the upgrade. (assuming there are benefits ;-) But s uch a course should only be for existing users who have to make the switch.