First of all some mysteries are good because they're so simple. The original Scream was a great mystery film because the killer does wind up being the first person anyone had suspected, the twist was simply that he had a partner. Now I'm not going to argue there are two Babylons (though I have argued there are two cities called the "Great City").
But I do feel a great deal of Eschatological confusion comes from people assuming Babylon is the Beast's capital. Chris White tying his Jerusalem as Mystery Babylon into his Antichrist as a Jewish False Messiah theory is dependent on that assumption. Same with the Pope as the Antichrist and/or False Prophet views.
Mystery Babylon wields power over the Beast, hence riding it, but the Beast later turns on her. I actually feel it makes little sense if that city is his political capital. I in fact feel there is no guarantee the Beast or False Prophet will ever set foot in Babylon personally, though they certainly could. The events of the Sixth and Seventh Bowls imply to me that the Beast is West of the Euphrates while Babylon is East of it.
This is also a good time for me to remind people that while I feel based on the importance of the Euphrates in Revelation as well as Zechariah 5, that Revelation's Babylon must be in Mesopotamia. I do not feel it needs to be the Babylon of Hammurabi and Nebuchadnezzar. Because I've already argued Eridu was the Babel of Genesis 10 and 11. And I find it interesting how H. G. Wells chose Basra for his Things To Come. Other cities that have rivaled Babylon as the regional capital include Nineveh (Nahum uses Whore of Babylon like terminology), Seleucia and Baghdad.
Ultimately though, the reason it's a "Mystery" is because while it is a very Specific City in Shinar it is also more then that, it is a Religious and Socio-Economic System. That has ties to other cities, but Zechariah 5 makes clear for the end She will return home. She is in a sense all False Religion.
I have responded before to Chris White's View. I agreed with White's point about how the Mountains are clearly linked to the Heads/Kings, and are not a separate symbol. But disagreed with how he used that as an excuse to render the Mountains irrelevant. I didn't know how to answer the Mountains issue then, but I do now since I have come to my finale conclusion on the Seven Heads and how they connect to Daniel 7. It could be we are dealing with not Seven Mountains physically near each other, but 7 Sacred Mountains or Hills for each of the relevant 7 Kingdoms, or all 7 of their spiritual capitals. Babylon, Persepolis, Alexandria, Antioch, Byzantium/Constantinople, Ctesiphon and Rome.
So Rome can indeed be relevant to understanding the full story of the Mystery. But she both begins and ends in Shinar.
The idea of removing Literal Babylon altogether and making Babylon a code for something else begins with Rome, other such views have been possible only because long held attachment to doing it with Rome made the idea seem acceptable. But none other then Rome started being seriously suggested till within the last two hundred years, three hundred tops. While the Early Church Fathers were often Anti-Semtic and held Jewish Antichrist views, you won't see among them a single example of a Jerusalem as Babylon view being suggested.
I myself have even flirted with allegorical Babylon ideas, mainly here. The main points of that post I still stand by. But any past confusion I had on Babylon has been cleared up.
The origin of viewing Babylon as code for Rome lies entirely in Catholics wanting to use it to make 1 Peter support their Peter was in Rome nonsense. The claim that Peter came to Rome I view as false, but it has ancient roots going back even to the second century. And Catholics are Ok with seeing Babylon in Revelation as Rome, they just insist it's Pagan Rome not Papal Rome (they will sometimes point out Vatican Hill is not one of the original 7 hills meant when Rome is called a City on 7 hills).
So that's why Protestants using a Babylon as Rome view against the Vatican is so annoying to me, they are actually using a Catholic lie as the foundation of their anti-Catholic Eschatology. If you can find a single example of a Catholic apologist disagreeing with Revelation's Babylon being Rome, I will be genuinely shocked, but one or two isolated examples would not undermine my point here. I was raised Catholic and the Family Catholic Bible has Babylon being Rome all over it's footnotes for Revelation.
And then we have Historicists saying that denying Babylon is Rome is a Jesuit deception (along with Futurism in general). Because Peter being in Rome is needed for the very foundation of Cahotlicism, the Catholics NEED Babylon to mean Rome at least once in The Bible, far more then they even care about Protestants calling the Pope the Antichrist.
So if you really want to hurt the Vatican, just accept that Babylon is Babylon.