The reason is that it mimics the way you would kill someone else most efficiently. The other answer saying disembowlment is "drawn out process" is true, but you don't disembowel them. Seppuku is not disembowlment. To explain...
First of all, the fastest way to kill someone easily with a sword is by slicing through the solar plexus. A large artery, called the abdominal aorta, runs longitudinally through the solar plexus. Severing this artery will cause a large decrease in blood pressure and put the person into shock almost immediately. Also, the solar plexus is a nervous junction. Severing it will generally cause an instant paralysis. Finally, just beyond the solar plexus is the diaphram, so at the same time you can flood the diaphram with blood, preventing any further breathing. In general, a cut of this type will instantly incapacitate the person (which is what is wanted) and they will be unconscious within less than 30 seconds usually, and completely dead within 5 minutes. Killing in this way is a much easier stroke than a decapitation (the next best option), and can be done at longer range.
Proper seppuku simply imitates this stroke. It is difficult to do because once the bushi cuts into the solar plexus he will become instantly incapacitated. For this reason the cut must be instantaneous and decisive. Any hesitation whatsoever will cause a failure.
Because of the difficulty of making this cut properly, often a less experienced warrior would cut at the navel below the solar plexus, more of a "disembowlment", however as long as the bushi severs the abdominal aorta, death will follow rapidly. The purpose of simultaneous decapitation by an aide is to prevent the bushi from involuntarily crying out--a dishonor. The aide must cut off the head at the exact instant the cut is made, otherwise the bushi may make a sound.
Below is illustrated the two possible cuts, the upper one being the correct and proper one, although more difficult to execute.
Note that the proper cut is quite near the ribs, so the bushi must be very quick, accurate and decisive to do it correctly and not touch the ribs. When delivering the same stroke to an opponent, it is much easier; the warrior just slashes upwards through the center of the body in a diagonal fashion as shown using the last three inches of the blade; this can be done on a draw, meaning by simply drawing the katana from its scabbard (the
saya) in the right way.
When committing seppuku, the bushi uses only the last three inches of the Wakizashi, holding it by the blade. A square of paper is wrapped around the blade so that the bushi can hold it without cutting himself.
When a woman or child was required to commit seppuku, they would make no cut at all. Instead, the folded Wakizashi paper (or a closed fan) would be held in the right hand and then touched to the stomach. As soon as the condemned touched the paper to their stomach, their squire (or the executioner, depending on the situation) would decollate them.