"Why do you need the program if you will conduct experiments to tell you the same answer? "
Because the experimental data is much more expensive than a stack of computer runs. If you even get to run transient tests, you are lucky; more likely you will calibrate your current job's computer simulations based upon either lab-generated experiments (for which you have a lot of data but the case modelled is rather simple, and there aren't very many of these cases to model, so..), or field failures (for which you will have limited data, many assumptions, etc.).
FWIW, I have no idea what the "Bond Graph" method is, but would agree with BigInch that it probably works just fine, and the choice of software is more about how easily it can be used for your anticipated work situation. The Method of Characteristics is well known, and described in a number of gas- and fluid-dynamics texts. To quote from a book on my shelf, Fluid Transients in Systems, Wylie, B. and Streeter, V., Prentice-Hall, 1993:
"For rapid transients in liquid pipeline systems the mehod of characteristics is generally considered to be the numerical method by which others may be judged for accuracy and efficiency. Other methods are available and in certain situations there are valid reasons to consider their use."
Personally, my fluid dynamics software consists of several dozen spreadsheets, some ancient fortran code that I occasionally dust off, some compiled codes that I can dust off if I ever need to, and some 20+ years of experience that lets me (usually) predict on the back of an envelope what the computer eventually tells me. Then we go try it in the real world, and Ma Nature grades my work.