Simply put, because the rubrics changed.

As for history, it was sung like this (I'm marking it as 1 and 2, which could be cantor/choir, or choir/cong, or choir1/choir2, whatever):

1)Kyrie
2)Kyrie
1)Kyrie
2)Christe
1)Christe
2)Christe
1)Kyrie
2)Kyrie
1)Kyrie

Depends on how you want to read the GIRM, especially that "or of other circumstances" part.

52. [...] Each acclamation is usually pronounced twice, though it is not to be excluded that it be repeated several times, by reason of the character of the various languages, as well as of the artistry of the music or of other circumstances. When the Kyrie is sung as a part of the Penitential Act, a “trope” precedes each acclamation.

In the OF the Kyrie may be sung either 6 fold or 9 fold. Both are correct, though the 9-fold is more traditional.

I have come to believe that a 9-fold Kyrie suits the situation where you have a small choir where you can have a cantor or Cantors singing with the rest of the choir responding.

When you only have a small group or even just a cantor a 6-fold is more practical as it is sung as a call-and-response with the congregation.

When I was talking about 6 vs 9 fold I was assuming the use of Gregorian Chant.

There are many mass settings which sing it 9-fold. Two that I have mentioned elsewhere are Mass in Mi (Bevenot) and Mass St Boniface (Wittal)

newadvent.org:

The first Roman Ordo (sixth-seventh cent.) describes a not yet fixed number of Kyries sung at what is still their place in the Mass: "The school [schola, choir] having finished the Antiphon [the Introit] begins Kyrie Eleison. But the leader of the school watches the Pontiff that he should give him a sign if he wants to change the number of the litany" ("Ordo Rom. primus", ed. Atchley, London, 1905, p. 130). In the "Ordo of Saint Amand", written in the eighth century and published by Duchesne in his "Origines du culte" (p. 442), we have already our number of invocations: "When the school has finished the Antiphon the Pontiff makes a sign that Kyrie Eleison should be said. And the school says it [dicit always covers singing in liturgical Latin; cf. the rubrics of the present Missal: "dicit cantando vel legendo" before the Pater Noster], and the Regionarii who stand below the ambo repeat it. When they have repeated it the third time the Pontiff signs again that Christæ [sic] Eleison be said. This having been said the third time he signs again that Kyrie Eleison be said. And when they have completed it nine times he signs that they should stop." So we have, at least from the eighth century, our present practice of singing immediately after the Introit three times Kyrie Eleison, three times Christe Eleison, three times Kyrie Eleison, making nine invocations altogether. Obviously the first group is addressed to God the Father, the second to God the Son, the third to God the Holy Ghost. The medieval commentators are fond of connecting the nine-fold invocation with the nine choirs of angels (Durandus, "Rationale", IV, xii). From a very early time the solemnity of the Kyrie was marked by a long and ornate chant. In the Eastern rites, too, it is always sung to long neums. It is still the most elaborate of all our plainsong melodies. In the Middle Ages the Kyrie was constantly farced with other words to fill up the long neums. The names of the various Kyries in the Vatican Gradual (for instance, Kyrie Cunctipotens genitor Deus of the tenth century, Kyrie magnæ Deus potentiæ of the thirteenth century, etc.) are still traces of this. As an example of these innumerable and often very long farcings, this comparatively short one from the Sarum Missal may serve:

Kyrie, rex genitor ingenite, vera essentia, eleyson.
Kyrie, luminis fons rerumque conditor, eleyson.
Kyrie, qui nos tuæ imaginis signasti specie, eleyson.
Christe, Dei forma humana particeps, eleyson.
Christe, lux oriens per quem sunt omnia, eleyson.
Christe, qui perfecta es sapientia, eleyson.
Kyrie, spiritus vivifice, vitæ vis, eleyson.
Kyrie, utriqusque vapor in quo cuncta, eleyson.
Kyrie, expurgator scelerum et largitor gratitæ quæsumus propter nostrasoffensas noli nos relinquere, O consolator dolentis animæ, eleyson (ed. Burntisland, 929).

[Lord, King and Father unbegotten, True Essence of the Godhead, have mercy on us.
Lord, Fount of light and Creator of all things, have mercy on us.
Lord, Thou who hast signed us with the seal of Thine image, have mercy on us.
Christ, True God and True Man, have mercy on us.
Christ, Rising Sun, through whom are all things, have mercy on us.
Christ, Perfection of Wisdom, have mercy on us.
Lord, vivifying Spirit and power of life, have mercy on us.
Lord, Breath of the Father and the Son, in Whom are all things, have mercy on us.
Lord, Purger of sin and Almoner of grace, we beseech Thee abandon us not because of our Sins, O Consoler of the sorrowing soul, have mercy on us.]

Notice the greater length of the last farcing to fit the neums of the last Kyrie, which are always longer. Sometimes the essential words are mixed up with the farcing in a very curious mixture of Latin and Greek: "Conditor Kyrie omnium ymas creaturarum eleyson" (Ib., 932*). The reformed Missal of Pius V happily abolished these and all other farcings of the liturgical text.

Voices of weak bishops are heard, saying: Hey, we've sung three, three and three since the 8th Century. Let's change it to twice! That'll help get one crowd out of the parking lot and another one in faster! Tradition? That's the stuff of Fiddler on the Roof, we don't need it.

Assuming that the congregation is used to repeating after the choir in a simpler chant setting, it would seem unrealistic by today's standards for the congregation to "intone" the first christe eleison in a nine-fold Kyrie. Perhaps 1: Cantor/choir, 2: congregation 3: choir (perhaps polyphonic?). 1:Cantor, 2: Choir 3: tutti would be even better, but that doesn't work for the final different Kyrie. Two trained choirs alternating makes the most musical sense, but when incorporating congregational singing it will depend on what they can realistically handle. Perhaps just having the cantor intone the first phrase and then having everyone sing the rest of the chant to the best of their ability is the way to go be it 6 or 9.