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Babylon is much closer to ancient Sumer (UR, Uruk, Eridu, etc.) than it is to the centers of Assyrian dominance (Nineveh, Nimrod, Khorsabad). A passage in Daniel would seem to indicate that Babylon was assumed to be part of Shinar.

In the third year of the reign of Jehoiakim king of Judah, Nebuchadnezzar king of Babylon came to Jerusalem and besieged it. And the Lord gave Jehoiakim king of Judah into his hand, with some of the vessels of the house of God; and he brought them to the land of Shinar, to the house of his god, and placed the vessels in the treasury of his god.
(Daniel 1:1-2)

Also, etymologically, "Babel" and "Babylon" are very similar in form, especially when you consider the absence of vowels in ancient Semitic languages. Also, in Ezekiel's prophecy of Gog and Magog, Magog (contrary to speculative modern views that it refers to modern countries such as China or Russia) almost certainly refers to Babylon. There is also a very good argument (which I won't go into detail here about) that "Magog" is an atbash (a type of word play) for "Babel" (similar to the atbash used in Jeremiah 51:1 for "Chaldea").

It would seem that the significance of the Etemenanki with regard to the Tower of Babel is that the Etemenanki was built on the foundation of an earlier ziggurat that would seem to date back possibly to the third millennium B.C. The less than typical tower-like proportion might also be of significance.

None of this is proof positive, but its possible correlation with the Genesis record is interesting to say the least.

Babel and Babylon seem to be just the Hebrew and Greek versions of the same name, Babillum in the Babylonian language.

In Genesis 11.9 where the KJV has the word Babel, the Septuagint text has Synchysis which means "confusion."

Babylon appears to be a very ancient site, but it was an insignificant place until the time of King Hammurabi in the 18th century B.C. The main Assyrian cities were further north near modern Mosul--there were periods when the Assyrians dominated all of Mesopotamia, but these were later than the time period the Bible envisions for the building of the Tower of Babel.

The Babylonian Empire of the time of Nebuchadnezzar is sometimes called the Neo-Babylonian or Chaldean Empire--they don't seem to be directly descended from the rulers of the first Babylonian Empire (there was an interval when an alien group, the Kassites, ruled Babylonia for several centuries).