Like ActionManly said - they were talking about period maps. Which means Philly was probably in the preliminary plans until they started their historical research.
If you don't believe me - look up some dev team interviews. It's not a big secret really.
They were planning on Philly being a central part - but the old maps of the city showed grid format. They picked Boston because the layout was more varied.
Plus, they said they aimed to make Desmond "cool" in this game. I'm looking forward to what they did - especially because they are being so tight-lipped about it.
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