Your grounds for skepticism match the heuristic that Anders Sandberg and Nick Bostrom propose in The wisdom of nature quite closely. They propose this heuristic to evaluate interventions to enhance humans, but it's clear that it has much broader applicability. Here's the relevant excerpt:

Suppose that we liken evolution to a surpassingly great engineer. (The limitations of this metaphor are part of what makes it useful for our purposes.) Using this metaphor, the EOC can be expressed as the question, ‘‘How could we realistically hope to improve on evolution’s work?’’ We propose that there are three main categories of possible answers, which can be summarized as follows:

• Changed tradeoffs. Evolution ‘‘designed’’ the system for operation in one type of environment, but now we wish to deploy it in a very different type of environment. It is not surprising, then, that we might be able to modify the system better to meet the demands imposed on it by the new environment. Making such modifications need not require engineering skills on a par with those of evolution: consider that it is much harder to design and build a car from scratch than it is to fit an existing car with a new set of wheels or make some other tweaks to improve functioning in some particular setting, such as icy roads. Similarly, the human organism, whilst initially ‘‘designed’’ for operation as a hunter-gatherer on the African savannah, must now function in the modern world. We may well be capable of making some enhancing tweaks and adjustments to the new environment even though our engineering talent does not remotely approach that of evolution.

• Value discordance There is a discrepancy between the standards by which evolution measured the quality of her work, and the standards that we wish to apply. Even if evolution had managed to build the finest reproduction-and-survival machine imaginable, we may still have reason to change it because what we value is not primarily to be maximally effective inclusive-fitness optimizers. This discordance in objectives is an important source of answers to the EOC. It is not surprising that we can modify a system better to meet our goals, if these goals differ substantially from the ones that (metaphorically might be seen as having) guided evolution in designing the system the way she did. Again, this explanation does not presuppose that our engineering talent exceeds evolution’s. Compare the case to that of a mediocre technician, who would never be able to design a car, let alone a good one; but who may well be capable of converting the latest BMW model into a crude rain-collecting device, thereby enhancing the system’s functionality as a water collecting device.

• Evolutionary restrictions. We have access to various tools, materials, and techniques that were unavailable to evolution. Even if our engineering talent is far inferior to evolution’s, we may nevertheless be able to achieve certain things that stumped evolution, thanks to these novel aids. We should be cautious in invoking this explanation, for evolution often managed to achieve with primitive means what we are unable to do with state-of-the-art technology. But in some cases one can show that it is practically impossible to create a certain feature without some particular tool—no matter how ingenious the engineer—while the same feature can be achieved by any dimwit given access to the right tool. In these special cases we might be able to overcome evolutionary restrictions.