If your not going to go crazy with the motor Tune ECU will be fine especially for maintenance it is free soft ware and a 20 dollar cable. PC units are ok but you do not get the advantage of being able to do the maintenance aspects of the bike. If you already have the PC unit and no one in the area can tune with the ecu soft wares available for the Rocket then at least you can load a good base tune for the bikes setup in the ecu and let them finish it off with the power commander unit.
So in a nut shell no tuning soft ware is better then the other. Just better suited for the particular application. And is limited by the tuners ability to use the particular software.
I must say I use Tune Boy but I have had it long before Tune ECU was out. I also do not really have a stock bike either. I am building one from a bunch of Rockets parts I have acquired over the years.