Why was it so special that John the baptist was not called Zechariah?
First of all, John and not Zechariah was the name to be given to Elizabeth’s new born.
Let us now look at what St. Luke writes about the birth of John the Baptist:
11 Then an angel of the Lord appeared to him, standing at the right side of the altar of incense. 12 When Zechariah saw him, he was startled and was gripped with fear. 13 But the angel said to him: “Do not be afraid, Zechariah; your prayer has been heard. Your wife Elizabeth will bear you a son, and you are to call him John. 14 He will be a joy and delight to you, and many will rejoice because of his birth, 15 for he will be great in the sight of the Lord. He is never to take wine or other fermented drink, and he will be filled with the Holy Spirit even before he is born. 16 He will bring back many of the people of Israel to the Lord their God. 17 And he will go on before the Lord, in the spirit and power of Elijah, to turn the hearts of the parents to their children and the disobedient to the wisdom of the righteous—to make ready a people prepared for the Lord.”
18 Zechariah asked the angel, “How can I be sure of this? I am an old man and my wife is well along in years.”
19 The angel said to him, “I am Gabriel. I stand in the presence of God, and I have been sent to speak to you and to tell you this good news. 20 And now you will be silent and not able to speak until the day this happens, because you did not believe my words, which will come true at their appointed time.”
21 Meanwhile, the people were waiting for Zechariah and wondering why he stayed so long in the temple. 22 When he came out, he could not speak to them. They realized he had seen a vision in the temple, for he kept making signs to them but remained unable to speak.
23 When his time of service was completed, he returned home. 24 After this his wife Elizabeth became pregnant and for five months remained in seclusion. 25 “The Lord has done this for me,” she said. “In these days he has shown his favor and taken away my disgrace among the people.” - Luke 1:5-25
Now we can deduce from the Sacred Scriptures that the emphasis should be on the name given to Elizabeth’s new born given to Zechariah by the Angel of God and not on his own name or one of his kinship as was traditional done.
Either name could have been give to the Forerunner of Jesus, but God willed that his name be John and Zechariah seconded God’s will!
Perhaps God did not desire the name of the Baptist to bare any association to his earthly family, but wanted it to reflect more his own divine intentions.
Any real reason for why God chose the name of John over Zachariah is not truly known to us and remains a mystery and is speculative at best.
English form of Iohannes, the Latin form of the Greek name Ἰωάννης (Ioannes), itself derived from the Hebrew name יוֹחָנָן (Yochanan) meaning "YAHWEH is gracious", from the roots יוֹ (yo) referring to the Hebrew God and חָנַן (chanan) meaning "to be gracious". The Hebrew form occurs in the Old Testament (spelled Johanan or Jehohanan in the English version), but this name owes its popularity to two New Testament characters, both highly revered saints. The first is John the Baptist, a Jewish ascetic who is considered the forerunner of Jesus. He baptized Jesus and was later executed by Herod Antipas. The second is the apostle John, who is traditionally regarded as the author of the fourth gospel and Revelation. With the apostles Peter and James (his brother), he was part of the inner circle of Jesus.
From the Hebrew name זְכַרְיָה (Zekharyah) meaning "YAHWEH remembers", from זָכַר (zakhar) meaning "to remember" and יָה (yah) referring to the Hebrew God. This is the name of many characters in the Old Testament, including the prophet Zechariah, the author of the Book of Zechariah. The name also appears in the New Testament belonging to the father of John the Baptist, who was temporarily made dumb because of his disbelief. He is regarded as a saint by Christians. In some versions of the New Testament his name is spelled in the Greek form Zacharias or the English form Zachary. As an English given name, Zechariah has been in occasional use since the Protestant Reformation.