There are a some flaws in your theory.

Mako for one thing only really exists in FFVII and to a much lesser extent, FFX. Other entries featuring crystals don't feature anything like it. Likewise the nature of magic doesn't work the same in all of the entries. Specifically in the case of IV and VII, magic is an inherit ability withing FFIV whereas magic is almost impossible to use in VII without a Materia as a medium for the power.

Secondly, Anna was also able to appear after death to guide Edward. Likewise, the King of Baron also returns from the dead and even transforms himself into Odin to help the party. So I wouldn't agree that Kluya's power at Mt. Ordeals is necessarily unique to an ascended race. Likewise, I don't feel genetics would even be able to play a part in being able to return in a non-corporeal form as consciousness as we biologically know it ceases functioning once the body dies. This definitely falls more into a spiritual type of deal of which evolution would likely not play a role. A good example here is how in VII spiritual essence takes physical form in Mako which is naturally occurring but then you go to FFIX where the crystal is pure spiritual and magical in nature and souls literally have to be processed into a physical form such as Mist to extinguish them so the crystal of Gaia can be forcibly merged with Terra's crystal.

Another issue here is that so little is even known about Lunarians that we really don't know how much of their ability within the story is some natural trait of their kind and how much could be simply a result of their advanced civilization. They are long lived, but is it actually a natural long life or simply the race using their advanced technology or knowledge of magic to extend it? I mean FuSoYa and KluYa are brothers but their age gap by looks is pretty huge, so it could be likely that KluYa looks younger since he was in stasis for awhile before being released and going on his mission to educate humanity while FuSoYa lived his life out naturally as a guardian. Likewise, we really don't get a real taste of how Lunarian genetics come to play until TAY with Ceodore who can temporarily access his Lunarian blood to temporarily enhance all his abilities, even then, it's likely his natural high aptitude with magic really comes more from Rosa's bloodline since Cecil is a sub-par mage especially in comparison to his brother and Uncle who both seem evenly matched in the power department when it comes to magic.

Finally, the Crystal dynamic is played inconsistently within the games themselves, so it's highly unlikely one games hot take on the subject would really apply to all of them. I mean ignoring the fact a crystal plays a major plot point in every entry, just sticking to the numbered entries that have a four crystals schlick within the plot, the crystals don't function the same way.

FFI - There are four elemental crystals that control the very natural order of the world, their corruption at the cost of the Four Fiends and Chaos are killing the planet and restoring their power restores the world. The crystals are non-sentient. There is also a fifth crystal of darkness used by Chaos, it's role is not completely known but is implied to be tied with his power over time.

FFIII - Eight elemental crystals, four in the realm of light, and four from the realm of darkness. They are sentient and represent the natural order of the world and it's possible to freeze time and space by manipulating their influence. Causing an imbalance of the crystals by flooding either world with too much of the others influence summons the personification of nothingness itself, the Cloud of Darkness, who is trying to return the world back to nothing before the crystals created everything. The crystals have the power to bestow the knowledge of classes to people.

FFIV - Their are sixteen crystals. Eight from the Blue Planet and Eight from the Lunarian world. Though the surface crystals are named after the elements like prior games, their purpose or abilities are never really gone into. The most they do is help Golbez and Zemus activate the Giant of Babil. The Lunarian crystals are sentient. We later learn in The After Years that the crystals are simply recorders for the Creator that help it witness and watch evolution on thousands of worlds.

FFV - Eight Crystals, four on each of the worlds. They are back to being elemental in nature and directly controlling the natural world. Their destruction means the eventual death of the planet. The crystals are sentient, but by the point of the story we only really hear the voice of the Wind Crystal. Like FFIII, the crystals possess the memories of past heroes and can grant their power to a chosen person to access it but things like magic are still natural forces everyone possess. The crystals are all physically destroyed along with most of the world by the power of the Void. The four virtues of the main heroes revive the original four elemental crystals and they restore the world back to normal.

FFVII - There are four colored Huge Materia based on the elemental crystals. They are manufactured by Shinra as a means to defeat Meteor. They are not sentient and their destruction doesn't really change the fate of the planet one way or the other. There are four natural materia as well but they only grant special powers.

FFIX - There are four Crystals, they are actually just shards of the Planet's Crystal which is the source of all life and goes through it's own cycle of death and rebirth. They have great magical powers but are not sentient. The Planet's Crystal possesses the memory of all life it gas ever known and can open a gateway through time to the original crystal that created everything. Like the Crystals in III and V, their is a fifth power that is strongly associated with the Void that comes in conflict when the Crystal is threatened.

FFXI - There are five crystals, all shards of the original Mothercrystal that is the source of creation. The five smaller mothercrystals created the gods and are used as a power to hold back the Void/Emptiness.

There are certainly similar themes going on here dealing with the five Japanese elements at play but the crystals are often a source of creation on par with being physical gods since their disruption or destruction spells absolute destruction for existence. The sole exception is FFIV where they serve a new function from the retcon in TAY. So I can't really get behind the crystal theory at all.

As for the evolution idea, it plays too much lip service to one game's world rules despite none of the other games really following those rules including the game it's technically a distant sequel to. While the series certainly has a lot of thematic elements and even a few literal elements carried across the series, the titles are just too unique from each other for me to believe the games exist within the same universe or timeline. I mean the Dissidia series itself pretty much confirms the games take place in entirely different dimensions which justifies why the game world physics work differently between entries.