Every model of bike can have a different result, but if I had to make some generalizations then I would say that both Dynojet & Factory Pro kits basically yield the same results they just do it in a different ways. For example (one brand may use smaller jets with thinner needles or one brand may use different springs without drilling the slides etc...)
Continuing my generalizations I would say that Factory Pro kits can usually be tuned a little more precisely than Dynojet kits, but with that comes the problem of getting some idiot that only half ass knows what he is doing trying to tune your carbs. Ya see anyone can install a jet kit, but knowing why we adjust the main jets, needle clips, pilot jets & mixture screws is the real key to making sure all the circuits flow together seamlessly providing linear power delivery.
Dynojet kits are typically easier to install even though they do usually require you to drill the slides.
Again the key is getting someone that knows how to tune the carbs for the right results instead of some guy that installed a jetkit once & now he thinks he is an expert...