If you have read the previous pipe theory, the 'history' of pipes were explored. But within this theory, I shall explore the nature of the pipes. To do so, it is best to explore some of the basic points of pipes.
It is a widely accepted fact, that Mario and Luigi discovered the Mushroom Kingdom through the usage of a pipe. Being that one ended up on Earth, which they discovered through a plumbing job. The pipe led them into that of the classic Mario Brothers game. The pipes allowed enemies to travel through the area and attack the two. Once they managed to rid themselves of them, they finally could safely proceed into the next pipe.
The pipes received a much deeper change in the Super Mario Bros. and SMB2 (Lost Levels), basic rules which never would really be changed. Many pipes could not be entered (which I will go into further on) and those that did, would lead to a whole different place. Some would dump the brothers in a underground area, underwater area, or simply spit them back out at another area nearby. The 'Warp' pipes were the same, but warped to much farther lands (some being to ones they had been to previously). And lastly, was the pirhana plants that lived within the pipes.
In Super Mario Bros. 3, the pipes served as a entry spot for enemies. Goombas of neverending numbers would warp out of the pipe. Pipes could be found on the map of the area, which would warp further within the land. Pipes played a signifigantly lower part in this game then the previous, except in the pipe happy land of 'Pipe Land'. In this level, pipes showed an extreme overgrowth. Even thinner pipes that were to small to enter. So many pipes that they would actually form their own landmass. But so many had no ends that finding a pipe to enter was difficult.
In Super Mario World, pipes played roughly the similar role in SMB3. Slanted pipes would also seem to 'project' the person out of the pipe. As if some sort of force was inside that pulled or pushed the person inside and back out again. Another situation was pipes that would actually move, getting taller and shorter. Also, in two of the boss fights, there was a set of short pipes which the enemy somehow could travel through without exiting the pipe and re-entering another one.
Super Mario RPG did little with pipes than what had already been done. Paper Mario, however added several interesting features. Some pipes would appear at the press of buttons, and would continue to grow to the pre-determined exit point. Several lose pipes could also be found within Mario's home, suggesting that they were installed somehow.
Lastly, in Yoshi's Island, many pipes could be entered. Some which fueled soldiers from unknown parts. Pipes, like in SMB3 and MB, were one more used as a source for enemy travel.
With these facts gathered, the basic elements seen from pipes are shown. Now we shall examine them in detail. By far, the most intriguing aspect of the 'pipe' is Pipe Land, from SMB3. As said before, an entire platform of pipes could be found. Furthermore, in Paper Mario, we see the pipes grow after being activated. Lastly, the dreaded dead end pipes that ended with just a block and went nowhere. What does this lead to? Part 1 of this theory is that pipes grow naturally. They may be placed by a individual, but after that they continue to grow until they empty out into another part. In areas such as Pipe Land, extreme overgrowth takes over the entire area. It is unknown how long it takes for pipes to grow, but it could takes hours to centuries.
Now, some other snippets of evidence. In the original Mario, most pipes, if not all, could only be entered one way. You could never go back down the pipe you already entered. In Super Mario World, the slanted pipes would blast Mario out of it like a canon. The second part of this theory is based off such. It is my opinion, that either air currents, a powerful ventilation system, or even some natural part of the pipe pulls or pushes the person to the other side. This prevents people from re-entering a pipe, as it would be impossible to enter. However, world map pipes on SMB3, SMW and all pipes in generalfrom the two RPGs allowed to go back and forth. These are clearly exception, which means pipes in some circumstances will change the current in an oposite direction when a person enters.
The final point is the Pirhana Plants that live inside. It is rather odd that these creatures live in pipes. You could speculate that their roots reach the other side. However, this is not the case at all. As we have all done many times before, pipes can be entered when the plant is still in the pipe. So the roots must not prevent passage, and curiously, the plant does not just consume the person inside. As noted above in Super Mario World's boss fights, only one solution can be provided. Cross pipes may be the only answer, holed in the side of the pipes that could slip into another one or just the ground. A small outlet within the pipe may be the home to the plant. As a mean of defense, it will crawl out of the whole and attack randomly. Alternatively, it is possible the plants possess the power to merely teleport upon entering the pipe. Deep roots, however, would be a definite must. Otherwise, the currents would suck the plant in and kill it off.
all in all, this is what has been learned... Pipes grow like Wheat, suck like Windows and are Home to Weirdos.