While critics of the Bible point out that this city as described here defies logic, one must remember that John is describing something that cannot be wholly understood and accepted by human senses or the human mind, much less communicated by human powers of description and explanation.
The city which the angelic messenger shows John is described by him as a large cube almost 1500 cubic miles. The only other place in the Bible we see a cube is the Most Holy Place of the temple (1 Kings 6:20). No one was permitted to enter there except the priest once a year after sufficient sacrifice and cleansing rituals. Here, the entire city is a sanctuary and enjoys the holiness and purity of the ancient Most Holy Place.
The wall, at only 216 ft. high, is low for a city this large but since the city is a cube it is hard to see how the wall surrounds it anyway. These numbers, 12 and 144, seem to have some symbolic significance considering their use in the rest of the book and the rest of the Bible. The combination of the foundations and the gates seems to signify that the people of God are all one people now (note also the plural use of “people” in v. 3).
The list of jewels appears to correspond to the list of jewels named as being in the breastplate of the ancient High Priest of Israel (Exod. 28:15-21). Philo and Josephus make much of the fact that these jewels also represent the twelve signs of the zodiac and the list here follows the signs of the zodiac in reverse. While some might take this as approval of astrology and horoscopes, such foolishness was condemned by the OT law and by the later prophets.
What this probably points to is that the horoscope is merely a pale mockery and copy of the truth and wisdom of God. What the horoscope can never do God himself does: he leads those who trust him by faith and he leads them into this heavenly city.
This city is made by God (v. 2) and the measurement, though revealed in human terms, we are to understand is perfection. We cannot judge God’s kingdom by human standards; we must measure by God’s.
God has made this city and the measure reveals it to be so. Just as God made this city, so God is forming his own people into a city whose measurement is to be perfection. Those who will live in this city must be those who are made, owned, and kept by the God who measures it. Though we see the weak, the despised, the outcast, brought into the church, we are reminded to that each of us is weak, despised, and outcast in God’s presence so there is no room for boasting.
This also means that just as God has built this city from the material he chooses, so he has begun building this city from those whom he has chosen. He also chooses how it is built, which is why he can say that it is only through Christ that one can enter into this city.
The city is his, the blessings of the city are his, entrance into this city is through his way and his means. We may wonder why God works as he does but we have no right to question why he works as he does or to change what he has revealed.
God builds his city and makes it perfect and so he will make us perfect, also. He takes those of us who fall short, who live in hypocrisy and sin, and he works through his Word and Spirit to make us who we are to be so that we are fit for this kingdom. He works in this age through Word and Spirit and Church to fit our spiritual selves and then fits even our bodies in the Day of Redemption.