Benefits of foot pedal kayaks include keeping the kayaker's hands free, using larger muscle groups than paddling and ease of use. Having the hands free is particularly useful when fishing, especially when there is wind or a current.
Keeping the hands free is useful for fishing because it allows the kayaker to cast his fishing line while he pedals. When paddling, a kayaker must stop before casting his line or cast the line while paddling with only one hand, which is less effective. When the wind blows or there is a current in the water, kayakers in foot pedal kayaks are able to keep the kayak in the same position by pedaling, which isn't possible in a paddle kayak.
Since foot pedaling uses the legs while paddling uses the arms, a kayaker typically generates more power pedaling. However, this doesn't necessarily mean foot pedal kayaks are faster than paddle kayaks. The seating position in foot pedal kayaks can lead to lower back pain, cramps and other injuries. Foot pedal kayaks tend to be easier to use than paddle kayaks, because pedaling is an easy technique to learn, whereas proper paddling technique is more difficult.
Foot pedal kayaks are typically more expensive than paddle kayaks. They have less storage space and cause slightly more noise.