Mystik, I can relate -
When I first played DF I was promised a game on unyielding complexity and infinite creation (the promise was not explicit, but those traits were certainly suggested by some of the reviews and responses I had read at that point).
At first, those promises held true! There was such a depth to the interactions I witnessed during play that I saw them as a reality unto their own. In other words, I truly thought of DF as an alternate reality and not a simulation.
Of course, those thoughts are silly. I was young and failed to understand those inherent limitations of the video game. Over years of play I slowly became aware of the boundaries of the simulation I was experiencing. Like you mention, rocks are a collection of properties and values and not just rocks. Dwarves are a similarly layered collection of traits, properties and values which are much more complex and varied than rocks. Compared to our shared reality outside the game, within the game of DF dwarves actually have much more in common with the rocks than with us humans playing the game.
I, too, experienced frustration about these facts. How could a game as complex as DF still fall so short of the ideal I had been promised? "A game of unyielding complexity . . " had become "A game with irritatingly meaningless specificity." Take wood, for instance. Different woods have different densities, but for the majority of purposes wood is interchangeable. Except for a few edge cases those densities are meaningless, and yet we still have to juggle and read through the different named woods.
However, I suggest you take a deep breath (before you completely descend into schizo-Nietzschean frenzy) and reconsider what you are asking of Dwarf Fortress, of Tarn Adams, and of video game development in general. To ask for a complete reality simulator would be asking for a completely alternate reality. That is impossible, and I believe it will always be impossible for a finite creature (human) to create an infinite reality (the universe). We can program patterns, we can program patterns that create new patterns, and program fractals and chaos in between, but at the top of all this creation is still just a human. You ask for a God, but where will you find that? Take a step outside, maybe then you might find something, but I doubt you will ever discover what you're begging for in the form of a video game.
You should understand that some of those things you demand are planned. Tarn Adams is competent in a fascinatingly complex way, and you can expect that he shares many of your broadcasted desires. If you take the time (breathe, friend, breathe) to read through the planned features of the game, you will better understand the outer boundaries of DF's simulation. For instance, you want randomized plants and rocks - that's planned! There will be a slider letting you go from Tolkien to Chaos and every state in between.
For now, you have two options to further your personal desires for the DF experience.
1. As indigopheonix mentioned, consider modding! Even simple .txt editing can lead to a completely new experience, and (as I understand it) further changes can be made through the utility DFHack. You have the vision, so make it reality!
2. Use your imagination to fill in the gaps. In the current version, you cannot explicitly simulate the formation of a new religion via mythological storytelling. However, you can recruit followers rather easily, and use your adventurer to build a church building. Your imagination can supply the story that you want to see. YES, I know that's not IDEAL but it's what we have and you must understand how brilliant it truly is. Nothing quite like DF, a complex simulation of materials and objects that can be used to help craft myth, has ever existed in human culture and you SHOULD FEEL COMPELLED to take advantage of that.
Mystic, you are an interesting writer and I hope you continue to visit these forums. I also hope you sit down and play the game and write out your thoughts. I, too, remember starting the game and being afraid to unpause. I was so damn excited! Your heart is in the right place, just try to calm down and see what brilliance you can create!