Metroids, a bio-weapon developed by the Chozo and Mother Brain to combat the X-Parasite, is a prime example of what NOT to do when you come across new life, new dangers, new challenges, and new ecosystems.
We all know the story of Metroid as a series. We know the dangers that arose, the battle for control of this life form, the damage this life form caused, and the resulting consequences of such a life form being created. What can we learn from all of this? Well, my take away is that you should leave well enough alone. Why do I think that's the lesson here? Let's explore it together to find out.
So first off, we know that the Chozo went to SR388 and found a functioning ecosystem. Strange creatures, and plant life seemed very well adapted to the planet. Among these strange creatures was the X-Parasite. We know the X-Parasite was deadly, and was a "body snatcher" of sorts. The Chozo were concerned by this powerful life form and the deadly abilities it had. So they created a life form to bring it down, the Metroids.
So how did they create it? No one knows for sure, but one theory video I saw (https://www.youtube.com/watch?v=6Oqgh-taKXE) explains how and why they created the Metroids, and the devastating effects of doing so. In fact that inspired this post a bit. The TL;DR explanation is genetic engineering of bacterial life to make a predator of the X-Parasite, and then it went crazy and destroyed a functioning ecosystem.
Okay with that out of the way, why would Nintendo even go this route? Why would they even have a lesson at all? Well I think it's a warning about over whelming push our species has in trying to play god with our world. We try to create bio-weapons that can be used to attack other nations, we pollute our environment and lead to all kinds of nasty effects, and there is a real possibility that our scientific discoveries and advances that we make in the name of making progress might end up being our own undoing.
Governments have been trying for years to create bio-weapons and genetically/chemically change these bio-weapons to create new and devastating weapons to unleash a utter hell upon their enemies. But what if these bio-weapons fell into the wrong hands as the Metroids fell into the hands of the Space Pirates? It could be harmful to everyone on the planet just as the Metroids are a galactic threat, not a localized one. Such a scientific advancement could be a disaster if gained by the wrong hands.
Look at the Prime sub-series, they experiment strongly with genetic engineering of space pirates using Phazon radiation/infusion. Many of the subjects died in the experiments unable to survive the infusion process or dying soon after infusion was finished. This is akin to the military experiments to make super soldiers using LSD and so on.
Also look at cloning which is clearly something that has been done in the Metroid universe. They try to clone Metroids to be used as weapons. They genetically modify them in Other M to take out the cold vulnerability to make them a powerful new variant to be militarized
So I think Metroid is a warning of sorts of the kinds of things that can go wrong when science is unchecked. Think of it as a modern Frankenstein story.