WARNING: LONG POST INCOMING...
Lol. Ironthunder1604, there's nothing wrong with having morals, and I don't believe morals are for people who enjoy losing. ^_^ While that it is true that going after the young is wrong, it's no different than what trainers currently do. The only difference is that wild Pokemon are shown as having a chance to fight back (and potentially fleeing). Trainers go and capture Pokemon without knowing if that Pokemon is fully grown, or if it's a parent that have offspring that needs to be taken care of. No one really thinks about it…it just is. In the case of an ancient Pokemon civilization, where human technology is not yet up to par in contending with Pokemon one on one, they have to come up with some solution to compensate for the disadvantage (and one way would be to get the young or the eggs.) Even though it's morally wrong, there will always be those few who don't care, go fulfill the task and bring back the prize. Afterwards, once breeding is well underway, no one would really think about how the commercialization of Pokemon had gotten started. Just as no one thinks about how products got on the shelf in supermarkets or by what means the jewelry stores acquired its merchandise. It just is and it's just there.
I would also add that in the role play, being in a world that has magical creatures, I would think there'd be elements/materials produced by the earth to help contend with said creatures that humans could acquire and develop in order to help establish a balance. There are magical items in the world after all. Take the normal world we live in for example. In various areas of the world, creatures (animals and bugs) exist that have natural predators to keep their numbers in check. Should a creature be introduced into an environment where there aren't any natural enemies, then the balance is thrown off and troubles (mild, moderate, or severe) often follow. On a much lighter side, as Titan500 mentioned the Sinnoh myths, here's one that explained why wild Pokemon appear in grass:
Long ago, when Sinnoh had just been
made, Pokemon and humans led
separate lives.
That is not to say they did not help
each other. No, indeed they did.
They supplied each other with goods,
and supported each other.
A Pokemon proposed to the others
to always be ready to help humans.
It asked that Pokemon be ready to
appear before humans always.
Thus, to this day, Pokemon appear
to us if we venture into tall grass.
So humans and Pokemon have/had a symbiotic (?) relationship. Also those snippets of folk tales that mention Pokemon being very close to humans and a Pokemon shedding its hide to sleep as humans is worth looking at.
I was also trying to work on an idea (either as a role play or a fanfic) that dealt with humans and Pokemon being one being, called Humons. They weren't like pokemorphs or ginjinka (sp?) or whatever they're called; Humons were just a different type of being. They were an advanced species who developed civilizations that were equal to or greater than Atlantis. They also developed transportation capsules (basically, ancient poke balls) that allowed them to transport a large variety of goods with little to no effort. These capsules didn't work on living creatures at the time. Then after some sort of catastrophe (or war), the beings that were one split into two (a fall from grace, so to speak). Now Pokemon (who were essentially the magical essence of the Humon) became an entity of their own, leaving the now empty Humons as mere humans with little to no magical abilities. This is why some humans possess telekinetic, aura reading, and other unusual abilities. A sort of compensation or byproduct is that humans would also naturally possess a heightened resilience that allows them to take an attack--say an electric type move--without instantly dying or sustaining permanent injuries (a type of nigh invulnerability). On
Pokemon Origins Red "caught" Charizard--which weights around 200+ pounds--without sustaining permanent injuries. Now, if one got body slammed by a Steelix it's safe to assume he or she wouldn't survive.
Returning to the story…many humans and Pokemon grieved over this separation, neither really knowing what to do to survive or exist. So humans and Pokemon depended upon each to in order to survive and to live. Some time after that great divide or the Great Rift as I call it, (the point at which humans forgot they were once one with Pokemon), a human or a group of humans could have become jealous of Pokemon and the power they wielded, and so started to war with Pokemon and/or trying to subdue them; humans attempted to (re)claim that power for their own. Some Pokemon felt sorry for the humans and didn't fight back (choosing to either flee or sacrifice their lives in a vain effort to turn the bad humans from their ways) while other Pokemon were less sympathetic and chose to engage their foe mercilessly. (In the present, this is why some Pokemon are helpful and others aren't.) Eventually, the humans used the (rediscovered) transportation capsules, after modifying it to enable the capture of Pokemon and hence the beginning of poke balls for capturing Pokemon.
This is getting a little deeper than necessary for coming up with a Pokemon role play, but it is fun to ponder on and think about. ^_^