Personally, I prefer the Power Commander.
I've done various forms of tech support/sysadmin stuff my whole career, and using 1 processor to modify the output of another before the data reaches it's destination just screams bad idea to me. BUT, I know for a fact that with the stock ECU, the bike will start and run well enough to get me home every time.
That means, if something fails, or I make a bad map, I can always get myself home by just unplugging some cables on the side of the road. If you mess up the ECU, you have nothing to go back on.
Plus, I try to make sure every modification I make can be undone, and reverted to stock. If I wanted to, I could undo every change I've made to this bike, except for painting the headers, and it would be the same as stock. Makes it much easier to sell later on.
Just my $0.02