Have an info dump. Not sure if all of it will ever be relevant, but I needed to get some of this stuff straightened out.

Aura and Auma

Most people tend to group them together, but they’re actually quite different. Auma is the creative energy, the yin part of the soul, while Aura is destructive, the yang part.
Auma is used in moves meant to heal health, remove status conditions, and increase stats. Aura is used to inflict damage, decrease stats, and cause status ailments. They can both be combined with a type and a physical action to create a ‘move’. If a Pokemon runs to low Aura or Auma, they can’t use moves that require that kind of energy. If a Pokemon runs low on both aura and auma, to keep them from straining themselves forwards they automatically shut down, or faint.
All Pokemon have an ability that, when certain conditions are met, automatically triggers their auma or aura in some way. For example, the Blaze, Overgrow, Swarm, and Torrent abilities are all very similar. As a Pokemon grows stronger, the ability stores a small amount of aura and auma away so it can’t use it. But when the Pokemon runs low on aura and auma, it releases the energy, temporarily giving them more strength.
Another example is Volt Absorb, Water Absorb, Flash Fire, Motor Drive, and Sap Sipper. These abilities let Pokemon absorb the aura of another Pokemon and convert it into auma for their own personal use.
If a Pokemon uses aura to use an attack, the aura will dissipate and break down into the world again as two things, pure energy and pollution. Pollution is corrupted aura. Shadow Pokemon have been known to use pollution as fuel for their Shadow Moves, as opposed to aura or auma.

Shadow Pokemon

Artificial Shadow Pokemon have had their emotions and pain sensing nerves shut down by artificial means. In addition, the decision making parts of their brain have been surgically altered. Their aura and auma both have been transformed into pollution. In addition, each artificial Shadow Pokemon has a secondary ability, called ‘Hyper Shift’. When an artificial Shadow Pokemon loses too much pollution, its’ ability kicks in, putting it into Hyper Mode. When in Hyper Mode, a Shadow Pokemon’s life energy starts being converted into pollution. The drain on their life energy puts strain on the Shadow Pokemon’s primitive brain, and makes them revert back to their primitive instincts, demanding them to lash out at anything that might cause further damage to them.
Natural Shadow Pokemon, although slightly rarer, are completely different than artificial ones. Natural Shadow Pokemon are Pokemon that experienced a pain so great, be it physical, emotional, or mental, that their pain sensing nerves shut down and their emotions became extremely filtered. This makes natural Shadow Pokemon more logical than regular Pokemon, and unlike their artificial counterparts capable of making the most logical decisions without being hampered by any kind of pain. In addition, instead of having their aura and auma converted to pollution like an artificial Shadow Pokemon’s, natural Shadow Pokemon have pollution, aura, and auma.
Shadow Pokemon of all kinds can be cured by many things. The most common one is making them feel an extremely strong emotion somehow, like fear, love, happiness, anger, or hatred. Really any emotion other than sadness will do. Sadness is the emotion that most often turns a Pokemon into a natural Shadow Pokemon, and will so do nothing to turn it back. As a side note, natural Shadow Pokemon do not have Hyper Shift as a secondary ability, and really wish to live a life as normal as possible.
Some aura seers have reported seeing a black aura around a Shadow Pokemon. The black aura is the presence of pollution in their soul. It is much easier to spot in artificial Shadow Pokemon than natural Shadow Pokemon, allowing many of the naturals to live their lives in relative peace.
It has been noted that roughly 3000 years ago a mysterious disease called the Shadow Contagion was created, which causes pollution to spontaneously spring up in a Pokemon. The pollution, if not quickly dealt with, transforms the infected Pokemon into a natural Shadow Pokemon.

Evolution

Growing up does not result from evolving. Rather, evolving is a result of a Pokemon maturing.
Some Pokemon, like most starters, evolve simply by growing up. By making a realization about themselves as a Pokemon, and embracing that decision.
Others, like baby Pokemon such as Pichu, Azurill, and Togepi, evolve through a particularly powerful emotion. It doesn’t matter which emotion, but it works best with a positive one like true happiness or mutual friendship.
Other Pokemon evolve due to an emotion invoked by a life changing experience, such as being captured, being released, being traded to an entirely different trainer, losing a friend, or gaining a friend. Something along those lines.
Meanwhile, there are certain Pokemon that require a dramatic increase in the amount of aura and auma they have. This aura and auma is typically drawn out from an item imbued with aura and auma. Examples of such items are evolution stones, and items like Sachet, Whipped Dream, DeepSeaScale, DeepSeaTooth, and Razor Claw.
Several Pokemon require a combination of the above methods, however.

Mega Evolution

The Ultimate Weapon drained the aura and auma of Pokemon, transformed it into pollution, and fired that blast of pollution all throughout the Pokemon World. It appeared to hit the Orre and Unova region extremely hard, causing not only the land to become a massive desert, but for the Shadow Contagion to spring up in both those lands. Unova has dealt with the crisis much better, it seems.
However, there was a secondary effect caused by the Ultimate Weapon. The stones of Geosenge Town had residual auma and aura left in them from the Pokemon killed to power the Ultimate Weapon. It is noted that when a Pokemon holds one of these stones, and a being they have a bond of mutual friendship or love holds a second stone, a ‘keystone’, a strange reaction is set off. The auma and aura in the stone the Pokemon holds goes from a dormant stage to an active one, fusing with the Pokemon, boosting their stats, giving them a new form to reflect those improved stats, and sometimes changing their ability and typing. It has been noted that the stronger the bond, the bigger the stat boost.
These stones have been dubbed ‘Mega Stones.’ It should be noted that they only react with a Pokemon of the same species as the one whose aura and auma it originally was.
Thanks to this recent discovery, the stones of Geosenge Town have become nicknamed a ‘Mega Stone Mine’. It has caused a massive controversy about the tiny town, with some believing that Geosenge should begin harvesting, identifying, and selling as many Mega Stones as possible, while others believe this would be desecrating priceless ancient artifacts.

HM Moves

HM moves don’t teach a Pokemon how to fly or swim. That would be silly. They just give them a critical boost of strength in a certain aspect of them so they can do for longer than average periods of time, or while carrying a trainer or Pokemon.
For example, Dive would let a Pokemon take a deeper breath of air and stay underwater longer, Fly increases the speed and height a Pokemon can normally fly by making their wings a hundredfold stronger, Surf makes a Pokemon swim faster than average, as well as creating a convenient current going in the same direction they are, Strength gives a Pokemon double their average strength for a short period of time, etc.
Most HM moves can be learned through years of practice, but trainers are impatient and downloaded the main ones as HMs.

Chaining Moves

Some moves are connected with others. If a Pokemon practices a certain move long enough, it may find a way to learn a more powerful version of that move. Wild Pokemon are capable of chaining moves like this, and learning moves that their species would normally never be capable of learning. There are even certain moves that lead to the signature moves of legendary Pokemon.
Certain moves also split into multiple chains. Many things depend on what chain a Pokemon will follow if this happens. Some things determining that are what type the Pokemon is, what items it’s holding, the environment it’s in, and what moves Pokemon around it know.
Trainers don’t know about move chaining because you have to start with the first move in the Chain, and trainers are impatient and usually just teach their Pokemon a crazy powerful move with a TM.

There. Hope that explains some stuff.
If you see an idea you like, and want to 'borrow' it, go ahead. I think it's interesting stuff.
Then again, my sanity is questionable in some areas.