According to a couple very reputable tuners on this board, they can tune a bike just as well with either.
The benefits of the ecu editor are that it has so many other useful functions, and it's still alot cheaper than a power commander that can only map fuel, ignition, and one set of injectors.
Some tuners just haven't played with the ecu editor enough, or don't want to try something unfamiliar.
I understand that not everyone has access to an ecu editor tuner, as the closest to me is 3 1/2 hours away.
You can use the ecu editor to turn off your pair valve, turn your fans on sooner, remove top speed and gear limiters, adjust secondaries on gen2's, and on and on. It basically gives you control of the all the ecu's settings, and you can always flash a stock map back at any time.
There is a $10 2 wire harness that plugs into 2 empty ports in one of the ecu plugs, and they connect to two empty ports in the black yosh plug, which is what you plug the interface cable into(it's only plugged in during the flash). The other end of the cable goes to your computer or laptop.
The 2 wire harness is almost invisible and takes up no space, and it's all that stays on the bike.
I have the ecu editor and I've removed the gear restrictions from my gen2 and 3 of my friends gen2's. One is a member here.
We can all tell you that the difference in power in 1st through 4th is alot, and especially 1st and 2nd.
If the ecu editor did nothing more than that I'de be happy with it. The restrictions are there to make the bike a little more tame for the average rider. As I said before, hard throttle in 1st or 2nd will loop you into road if you let it.
I'm not arguing or yelling either, just passing along what great thing it is, and that it's worth checking out.
It's the next thing to do after what you've already done to gain more power(it works great on a stock bike too), especially since it can handle ANY future modifications you make to the bike in the future.