I don't think it matters whether its tuneboy, rexxer, rapidbike, microtec, or motec or MM. So it doesn't matter if it 'allows mapping while the motor is running', or o2 sensors, or something is rebadged or not. I mean MM allows their ECU's to be rebadged as well.
The real issue is the ends justify the means. You want something that can be tuned to what you are running (manifold, exhaust, etc). It doesn't matter if its the most closed system in the world, but if it can be optimally tuned based on your particular configuration.
I'm pretty certain that most of the "good" tuners can take any of those above ecu's and tune a bike to be optimal using a dyno. And some of those can "turn the fan on at a certain point" or print your name out across the dash on start if you want. But thats not the point - its to get a particular bike to run as close to optimal - and if they can do it with dyno runs while the bike is running, while they are off the bike, or pull the values our of their arse in their sleep - doesn't matter. . You just want those bits in the ECU to be tuned for your bike.
So, in that regard my opinion is and has been - that you want the best tuner. Not necessarily the best tools. The tool just has to be adequate for the job, the tuner knows what to do with the tools. Simple tuners will just muck with the AF to get close to 13 and thats it. Good tuners know what you want and can make the changes necessary. Some tools might be better than others, but by and large - we aren't going to use the tools all that much, the tuners are.
If you want the best tools - the tuneboy, rexxer, rapidbike etc don't hold a candle to the motec/mm/pi/cosworth stuff that can tune a bike and work with data loggers to give you the complete picture. But is that what you need ? doubtful - you just want the best power/torque curve for your manifold/exhaust combination on your bike.
