Dear Nassir,
OK, I will now go down to Astronomy 101 level, and explain very simply how scientists discover facts about any planets.
1- They discover planets with telescopes (systematic search and sky survey)
2- They photograph it on daily or very short intervals
3- They observe and measure (with very high precession) the changes in the position relative to star background
4- With mathematical formulas (which God has crated and scientist discovered it only) they calculate the orbital path and distance from the sun.
5- Same way the object motion declares if it’s been affected by any other close by objects or if it has any moons
6- With Pluto case it was very clear to estimate it motion and orbital path as it was observed on very long period of time (since the discovery in 1930) and data is very accurate, so accurate that today any good astronomical program like Starry night or similar can project it path and predict it’s location in the sky with pinpoint accuracy, same way do the GOTO telescopes, if you aligned you scope properly (12” Telescopes) you can observe Pluto from your backyard.
Now after this basic introduction, let’s put facts together:
1- Pluto is not moon of Neptune, as if it was then motion of Neptune and Pluto will show it clearly with telescopic observation
2- Observing Pluto shows very clearly that it orbits the sun not Neptune
3- These object called Trans-Neptunian, as these object orbits cross Neptune orbit.
4- Many objects (10,000 objects till this day) have been discovered in this region (Kuiper belt) all of them orbit sun.
5- Scientist have found bigger object in same region and called it Eris, with diameter of 2400 km, and it orbits the sun not Neptune.
Distinguishing between Scientific facts and Scientist speculations:
Scientific fact is observation and direct calculation results
Scientist speculations are rough estimation and conclusions which need observational proofs to support it so it may or may not become fact.
The example which you have mentioned about Pierced shower, it’s very difficult to any scientist to say with factorial level how it would appear, as the meteor are very small and cannot be observed with telescopes from ground or space (meteor size pebbles to dust only).
You example is not in correct place.
Yes calculating exact mass and size of objects far away in solar system is difficult, but the variation is very small, it would not exceed 5% at extreme case, we can wait and see what results will come out of Pluto mission at 2019.
This is not correct for prediction of orbital path, as motion is very clear and has been observed for so many years, so with very high accuracy any one can predict the location of Pluto at any day of year.
You said:” Wherever Neptune goes, Pluto is with it; keeping some distance from Neptune. (Like our Moon and Earth.) ; i.e. Neptune rotates around the Sun carrying its moon (: Pluto) with it; just like our Moon going around the Sun, but of course carried by the Earth, around which it rotates.”
We say: this is illusion not fact as if you plot the orbit of Pluto based on astrophotography only (1930 till today) you can see clearly that it is not following Neptune.
You said:” Pluto rotates in the opposite direction from most of the other planets.”
We say: My friend please note that Pluto orbital motion is in same direction of all planets, it’s axial motion is on opposite direction only, and even if it was rotating in opposite direction this is not proof that it orbits Neptune, if you have new theory on this issue please give us mathematical or observational facts.
Please see this link: http://cseligman.com/text/planets/plutorot.htm
You have misunderstood what this link is trying to explain “Pluto's Orbit http://www.nineplanets.org/plutodyn.html” this link is showing that Pluto and Neptune will never collide or even change each other orbit in any time as there orbits are very stable, please read it very carefully.

You said:” Therefore, the study of this subject, with an eye of a teacher, will give all of us more chances of discovering the truth, and add many new things to the science of Astronomy.”
We say: What do you mean by teacher eye? Do you have new criteria for astronomy or scientific research? , discovering truth is done by observation in astronomy not by speculations and theories.
Again I’m requesting you do not mix science with religion unless you are master in both fields and have solid backgrounds especially in fundamental physics.
Regards
Hasan Ahmad