IR and RF both have their own advantages and disadvantages.
Both are subject to noise interferrence. IR is subject to interference from IR noise from sources like compact fluorescent lamps, plasma panels, etc. RF is subject to interference from RF noise (too many sources to list). Which will be easier to implement, and more reliable, will depend on the environment.
The line of sight limitation of IR can be a disadvantage or an advantage. It is not really line of sight because IR can be reflected by walls and such. But on one hand, you may have to use a repeater. On the other hand, you may be able to have two completely independent systems in the building, using similar components, as long as the IR signals cannot get from one area to the other. To do this with RF, the two systems would have to use different frequencies, command codes, or something else to keep them from interferring with each other.
IR technology is simpler than RF. So the hardware itself, is likely to me more reliable than with RF. But nowadays most of this stuff is pretty darn reliable anyway.
IR requires running a wire from the target to where the signal is needed. This may be trivial or a big deal depending on the environment. RF just requires a receiver that gets an adequate signal where it is located. Sometimes getting that adequate signal can be a problem.
FWIW all my audio/video gear except the display and speakers are in a closet off a hall connecting to the viewing/listening room. I have a single IR target that is about 30' away from the back wall. I can control the system reliably standing in the middle of the room, facing the back wall. So the signal has to travel at least 45'. Just have to have the right remote.
