The coil on plug ignition uses a cam sensor that sends a signal to the PCM. The PCM then fires three coil packs one at a time. There is one coil for two plugs, and the coil fires both plugs at the same time, because of this there is spark on the power and exhaust stroke. This design is simpler because of less moving parts, and less wear items (spark plug wires, cap, rotor). It may be less sensitive to water.
Here is why this design sucks. Because of the three coils, if you plan on using an aftermarket ignition, you have to use a controller that is a lot more expensive (an MSD DIS vs. 6A). There are no high performance coils made for this system, and if the coil rail goes bad, it is a lot more expensive than the single coil used by the conventional ignition.
The later model PCMs that use the coil on plug ignition also control the transmission. That might cause some problems. It also has more emission controls (that is why they added the intake to keep the HP the same).
If you look at it from a $/Hp standpoint, it would be an expensive upgrade. You would see much bigger and cheaper Hp gains by putting an aftermarket ignition controller on your stock system. Then you can have multiple spark, and a rev-limiter.