Yet, what you don't realize is you sacrifice individualism, uniqueness, and the ability to be different and disagree. You promote uniforminty and homogeneity as a means of solving the problem of organics being "chaotic" by nature, creating synthetics, and then destroying everything. That is not a choice for the Catalyst to make. That is not a choice for Shepard to make. Nobody has the right to play God. Let the galaxy work it out through natural means under Destroy.
There are several questionable assumptions in your reasoning.
First and foremost, all life on Earth shares the same DNA. That, as observational evidence shows, does nothing to reduce diversity of life, or individual differences of all kinds in humans. Thus, making organics and synthetics connectable on a molecular level does nothing to preclude diversity of life or of thinking.
Second, the difference between "natural" and "artificial" is a delusion. Organics and synthetics alike are both completely "natural", since nothing we can build, being natural ourselves, can not be natural in itself. This delusional dichotomy is itself the result of ideologies that place a particular kind of sacredness on the so-called natural, based on the assumption that life's deepest roots are, and should forever remain (alternatively: inevitably will forever remain) untouched by human artifice. However, that self-aware synthetics exist in the ME universe proves that we can create life and that this basic assumption is false. The typical way out for proponents of that reactionary ideology is to claim that synthetics aren't true life. Well, you can do that, and then of course you would never choose Synthesis, but I would question the value hierarchy behind such a decision.
Third, as for "playing God", that's a typical phrasing coming out of the same reactionary ideoiogy that claims the roots of life should remain untouched by human artifice. At the end of the ME trilogy, we are not "playing". We are called upon to assume a god's responsibility whether we like it or not. Every choice we can make is of that kind. Regardless of the choice you actually end up making, if you think one of the choices is fundamentally better than another, will you really refuse to make it just because you are, in fact, assuming a god's responsibility, determining the fate of all life in the galaxy? Making a decision about making a fundamental change about the biochemistry of life is no different than making a decision about becoming an AI god or consigning a whole domain of life to extinction. People just feel different about it because of our cultural history of seeing the so-called natural as sacred. This idea, btw, is less than two-hundred years old, being a legacy of classical romanticism. It is a legacy that, as Shepard, I am glad to consign to the graveyard of cultural history.
So in the end, you may or may not see Synthesis as the best choice for the galaxy, but your stated objections are a flawed basis for judging its merits, rooted, as they are, not in evidence but in your own preconceptions. You can legitimately answer the question "Do I dare make such a fundamental change" with "no", for various reasons, but your assumptions about the outcome are flawed. You can, of course, fear such an outcome and decide not to take even a small risk of creating it, but there's a similar risk of bad outcomes of different kinds in every other decision: will Destroy ultimately result in the extinction of organic life? Will Control-Shepard become like the Catalyst? Assuming that there is a risk of either, I can refuse to see those choices as valid just as easily.
Personally, I choose Synthesis because it's the most interesting outcome. The others are variants of things people have done to solve problems for time immemorial: killing and autocratic rule. Synthesis does something new. I prefer to risk jumping into an unknown future.