I wondered the same, but it really, for me anyway, came down to convenience.
I am not that technical so I don't do much more than the batch operations of backing up, verifying my backups and restoring apps after loading a new rom. With the pro version I am able to do my restore with basically the one click to kicking off the batch run rather than having to agree to installing each app individually.
I am sure there are others out there that can answer to the more advanced options
I'm not sure if its still this way, but the Pro version lets you freeze system apps and such and the free version does not. I have not used the free version in a long time, but I think this used to be the case.