Within Shmoneh Esrai we daven for everyone of these items below, except for childbirth. Why?
R' Yochanan said: Three keys the Holy One blessed be He has retained in His own hands and not entrusted to the hand of any messenger, namely, the Key of Rain, the Key of Childbirth, and the Key of the Revival of the Dead. (Taanit 2a).
I would venture to say that the two out of three which we do pray for, rain and techias hameisim, are completely out of our ability to control. Having children, however, is something which humans are involved in.
Now of course this begs the question what about other brachos in Shmona Esrei which are also accomplished through human action, at least sometimes, such as Rifaeinu.
But I will point out the following regarding these three special items which Hashem Himself has the key for, and based upon this you rightfully argued should have all been included in Shmona Esrei. The two that were included weren't put into the sheilas tzorchav, requests for ones needs, section of Shmona Esrei, as was Rifaeinu. They were put into the section of shvach, praise, not bakashos or hodaah. Mentioning something a human can be involved is not shvach of Hashem. Therefore fertility was left out.
Of course if someone needs to be healed as far as fertility goes, they can always put in a personal supplication in its proper place.
