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Genesis 11 says that "came down" to see what was going on. Does this reflect and antiquated notion that heaven is literally "up"?
If so, it is hard to see what the problem would be. Even today the heavens are "up" from our perspective, and the best view in any event is always going to be "down". Would it make any more sense to say that God could also stare up through the earth?
At the same time, what probably motivates the "come down" language more than theology is poetry. No, not in the sense that the scene is figurative, in the sense of ancient poetic-literary patterns.
The Babel story is laid out in the form of a chiasm -- an ancient literary technique that aided in remembrance. The "go down" is a parallel back to the men's "go to" in 11:4.
Similarly, "let us make bricks" parallels to "let us mix up" -- there's also a pun there, since bricks in Hebrew is nilbenah and "mix up" or confuse is nabelah. This is literary craftsmanship.
Another objection is that God didn't come down on other tall structures like the pyramids of Egypt or the ziggurants of Mesopotamia. But tallness had nothing to do with the Babel story. The ziggurats were designed to look like step-ladder edifices that formed a stairway between the gods and the earth [Matthews, Genesis commentary, 471].
Design and purpose, not height, was the issue at hand. A physical ascent was not intended; even in Babylon the intent was symbolic and the "reaching" achieved by spiritual and ceremonial methods. Form was dictated by function.
The first Babylonian ziggurat was called Esagil, or "house with the raised head" -- Wenham, Genesis commentary, 235ff. Let us note further that making a tower with its top in the heavens didn't require a lot of height, by the ancient definition of what the heavens constituted -- basically, any fair distance above the ground.
In light of the purpose of the ziggurat, the idea was that men would empower themselves by being able to ascend to the divine -- not physically, walking up the side of the ziggurat, but by spiritual means. The desire not to be scattered is in direct rebellion to the earlier command to "fill the earth", which would require being spread out. Man is depicted as defying God's order and of trying to take matters into his own hands by reaching for the divine.
Others say Genesis 11:9 errs in its etymology: "Babel" means "gate of god," not "confusion" or any such thing as that.
In a sense this is correct, but it is doubtful that ancient writers intended such etymology to be taken literally anyway. Puns and wordplay were par for the course in the ANE. Babili means "gate of the gods"; balal means confusion. The play on words is not a serious etymology, not even a folk etymology, but a subtle dig at Babylon's own name for itself.
Wenham adds that "gate of the gods" is probably not correct either, but rather Babylon's own attempt at what might be called a "folk etymology".
In terms of the argument that the story gives us polytheism because it says, "let US go down," see here. Note as well that the "let us" is a parallel to the "let us" of the men in the chiastic structure of the story.