Why is St. Stephen acclaimed as First Martyr, not the Holy Innocents?

A question of this sort is astute. Martyrdom in the Church is a very sensitive issue and while not debating this it is worth noting that not all are called to die a martyr's death in order to see the Lord 'face to face'. Meanwhile, we can die as martyrs if we die to our ways of sin. 

A martyr (Greek: μάρτυς, mártys, "witness"; stem μάρτυρ-, mártyr-) is someone who suffers persecution and death for advocating, renouncing, refusing to renounce, or refusing to advocate a religious belief or cause as demanded by an external party. Martyrs play significant roles in religions especially in the Catholic Church. 

The Church celebrates Martyrs. Every 26th December is taken to be the veneration of St. Stephen who was stoned to death as recorded in the Acts of the Apostles (cf. Acts 6-7). The Church in the mood of martyrdom celebrates the Holy Innocents every 28th of December. 

St. Stephen is acclaimed as First Martyr (Protomartyr). The problem lies in why St. Stephen is said to be the first martyr and not the Holy Innocents. The Holy Innocents were the children (2 years and below) spoken of as being killed by command of Herod in his quest to eliminate Jesus, the new born king (cf. Matthew 2:13-18). By normal reasoning the Holy innocents are to be the first martyrs, why St. Stephen? 

The difference lies in the undeniable fact that Stephen died by free will, blood and love. In the case of the children they died by blood alone

Love at its purest and most selfless is demonstrated when there is a full knowledge coupled with a full willingness to give of oneself  (Fr. Luke Fong). 

Another debatable and controversial issue lies in the number of children who were killed. The Greek Liturgy notes 14,000 boys; the Syrians note 64,000 while the Medieval authors record 144,000. Modern writers reduce the number since Bethlehem is relatively a small town. Josephus Flavius, however, did not record this act of Herod but relates quite a number of atrocities committed by the King during the last years of his reign. The number is not certain. 

The Church celebrates the children as martyrs (flores martyrum). Only the Church of Rome calls them Innocentes but other Latin countries simply calls them Infantes.