Meaning no disrespect whatsoever it really is nothing like a yak. The yak is designed to run forward with the current thru the rapids, albeit resting and doing tricks and stuff (or so it appears to me, a non-expert). The raft on the other hand is designed to hold against the current and even paddle backwards upstream in moderate currents, thus creating a great platform for flyfishing and traveling from spot to spot at a speed that is some fraction of the current speed. You pull the oars like a driftboat, not dig like a yak. Pontoon boats are incredibly stable, we're talking stand up and fish stable. They maneuver very well due to the rocker but get blown around by wind pretty good on lakes and open water as the cost of doing business on river currents. Kayaks, with the exception of the tri-marans and tandems, are not all that stable in comparison.
For salt and stillwaters I would say the kayak is a clear winner, but for fishing in rivers the raft is almost as good as a driftboat, and better than one if you don't fish from the boat but only use it to get to the choice spots along a length of river.