Has anyone considered that Materia seems to be a natural phenomenon occuring due to the lifestream? By this I mean that the lifestream is independently taking any and all knowledge that resides in the lifestream and crystalizing it into materia. It doesn't seem to only be choosing things based on their usefulness or or some cetran intent. It stands to reason that merely having a cetra, or group of cetra, inadvertantly discover that it was possible to do such magic, theoretically, would insert that knowledge into the lifestream upon death. This would allow it to be crystallized regardless.

I'll simplify using a real world example. Suspend disbelief and assume people on earth were wholesome crunchy granola peace lovers. Assume that we used fire to heat our homes, electricity to power our world, water to control erosion, irrigation, and landscaping. When we died, knowledge of these elements were then turned by the earth into materia. The resulting materia could be used as combat magic, totally independent of their original uses. Materia merely provides the understanding of how these elements could be influenced. Now lets say in the 40's nuclear power is discovered, and when attempting to harness it's use for mankinds benefit, someone had a brief realization of the possibility of an atomic bomb. Now, because of that flash of realization, when this person dies, that knowlege is also crystalized along with his other nuclear knowledge. If someone were to find that materia, they would also theoretically be given the framework for how nuclear energy could be harnessed for destruction as well. A noble goal that resulted in a terrible realization, was reproduced via materia into something akin to an a-bomb materia.

I always assumed this was the case in FFVII. The cetrans may have been studying astronomy, or developed a spell to divert errant asteroids from the planet. When they died, this was distilled down to "materia for controlling the trajectory of massive objects in space." That generation probably realized its threat outweighed its possible good, and stopped that line of research to prevent further knowledge of it. Future generations would have realized the terrible power of the materia when it appeared, and chose to seal it away for the same reasons. Without using it or continuing to develop that magic, it would have kept the saturation of that knowlege in the lifestream minimal, supposedly enough that it only crystalized the one time.

Just my thoughts on a possible explanation.