There is a well known disagreement, or possible confusion, about what the true miracle of Channukah is. Most people are familiar with the story of Channukah regarding the miracle of one jar of oil burning for eight whole days. This story can be found in Massechet Shabbat (21b). However there is also the additional prayer that we add to the Amidah and Birkat HaMazon , על הנסים, which does not mention the miracle of the oil at all. Rather this additional prayer focuses on the other miracle that happened during Channukah, the miracle of the military victory against the Greeks. The question that can be debated ad nauseum in Yeshivot is: which is the true miracle of Channukah, the oil or the military victory. (In Yeshiva-speak it would sound like: Which is the ikkar - נס פח השמן או נס מלחמה?)In true Modern Kabbalistic Chassidic (and even possibly post-modern) style, this is not a disagreement (מחלוקת) that is meant to be resolved. The tension between the two miracles reflects two fundamentally different approaches to describe how HaShem interacts with the world. The miracle of the oil is an obvious miracle which contradicts the laws of nature. It is scientifically impossible for one jar of oil to burn for eight days. This type of obvious miracle is called a nes galui (נס גלוי). The miracle of the military victory is a hidden miracle (נס נסתר) - although it is improbable for a small band of Maccabees to defeat the might of the Greek army, it is scientifically possible. See my blog post for a discussion of the Ramban's explanation of hidden miracles (נסים נסתרים).
Now let us return to the question of why does the additional prayer (על הנסים) only mention the hidden miracle of the military victory? I would suggest that Chazal felt that it is only appropriate to daven for hidden miracles. There is a Rabbinic aphorism - על תסמול על הנס, do not rely on miracles. When we ask for help from HaShem we should not ask for outright miracles that contradict the laws nature.