From the user point of view, there is no difference between fly-by-light and fly-by-wire. The primary advantage for fly-by-light is that it is basically immune to EMI/Lightning effects (there may also be some small weight savings if they can get the connector thing figured out). The primary disadvantage is currently the connectors - no one has really come up with a lightweight bulletproof aviation fiber optic quick disconnect that's good for the life of an aircraft.
Fiber optics have been used on IFE systems (starting, I believe, with the original 777) but IFE is generally not considered flight critical.
Boeing did a project back around year 2000 where they installed fiber optic throttle resolvers on a 757 for in-service evaluation (it didn't actually control the engines, just fed a box out on the engines that recorded data). Throttle resolvers are a particularly attractive use since the wiring goes outside the pressure vessel and hence is exposed to the full EMI/Lighting threat - but it's also a very difficult challenge for the connectors since the on-engine connectors are frequently disturbed in a potentially dirty environment..