My oh my!!! Tuning an engine is not about being able to use software: it is a procedure requiring understanding engine dynamics, how variables affect those dynamics, and then how to isolate them sufficiently to adjust one without impacting others without knowing you are doing so. The software is nothing more than a sophisticated wrench. Tuning is a skill that requires intelligence, knowledge, "feel" as in seat of the pants, and practice.
Much of the problem can be traced back to Dyno-Jet and their marketing. "Anybody can tune with our easy to use equipment and software. One hour and you can make $300.00." What an effing load of bull!! Many people cannot do it well no matter how hard they try.
Pulling several full throttle runs which last maybe 4 seconds each, checking a readout showing A:F ratio, and declaring the tune is good once adjusted to a constant 13:1 is not tuning. It is a test only of full throttle operation at a prescribed acceleration rate! If you go looking for the biggest numbers and that is the only thing you want, tuning is easy. But you may not like riding your bike home.
News flash: Some motors run and perform better at full throttle when the A:F is not constant. And no one, not even drag racers run at full throttle only.
Inertia dynos are severely limited in the data that can be garnered from their use. They are simply one tool available to a tuner. Experience with the particular engine family is very important. Taking an R3 to a Harley tuner who has never ridden a Rocket before is just begging for a crappy tune. Not that he or she can't figure it out but expect your bike to be ridden multiple times over several days. Maybe after about $1,500.00 and three days you might have a reasonable tune if the base tune is close to start with and if the tuner is good.
Consumers also have some unrealistic expectations. There is an expectation that a "tuner" can do in one hour what took a team of OEM engineers weeks or months to accomplish. Secondly, the al e carte shopping for performance parts can and often does result in compromised performance that no tuner can magically correct.
Using a tuner who speciallizes in tuning your brand and type of bike is the most effective use of your money. Call them first, BEFORE BUYING ANY PERFORMANCE PARTS, and ask them what works, what doesn't, and which pieces work well together to achieve what you want to accomplish. Then listen to what they tell you. You will be much happier in the end.