Back when the satellites of the outer planets were the only other Pluto-like objects known, this was a likely hypothesis. Now, however, a great many other Kuiper belt objects have been found, such as Quaoar and “Xena”, and some of those have even crazier orbits than Pluto. Unless Neptune kicked them all out of the ecliptic, it’s more reasonable to assume that the Kuiper belt objects were just less tightly constrained in the first place.
And there were observed discrepencies in Neptune’s orbit, and calculations resulting from those discrepancies did, in fact, lead to the discovery of Pluto. It turns out, though, that that discovery was purely fortuitous, and the discrepancies observed in the first place were just experimental error. While the planets do in general have measurable gravitational effects on each other, and Neptune certainly has significant effects on Pluto, I would very highly doubt that Pluto’s effects on Neptune are at all significant (as in, we probably couldn’t even detect it with specially-designed probes in orbit around Neptune and Pluto, using the most advanced cutting-edge technology even currently on the drawing board).
Oh, and Quartz, I won’t say that the ApJ is above playing an April Fool’s joke, but if they did, it’d probably be a lot less subtle than that. And the scientists who write a scientific paper have very little control over when exactly that paper will be published. So until and unless we see a retraction, I’m inclined to trust that cite.
Let’s not forget the Oort Cloud or spiral galaxies’ halo objects (stars and star clusters). These are objects that are spread more or less into a sphere around the disc of the other objects. Oort Cloud objects around a planetary system, and halo objects around a galaxy.
With such long orbital periods, objects at the outer edges of the solar system will have had fewer chances to interact with their neighbors since the formation of the solar system.
