Regardless of which method you choose,dyno tune is always the preferred option because that applies purely to your bike and not just a generic map.
It also depends on how far you want to go.Just to optimise an exhaust,change traction control,change how the throttle works compared how much the ecu says you can have,removing factory nanny settings-the list is endless.You can,of course,alter everything yourself with hp ecu/rck(if you knew what you were doing!).
If you just want the basics then dyno tuned Power Commander or similar is probably favourite but,if you want more then either someone like Phil Crowe or an RS2E remap or(in my opinion,having used one in 2012)a Brentune handheld unit,albeit custom mapped via email whilst on the dyno.