Locations within Fuyuki can still be important in that they're where shit happens, but I suppose they're just as easy to do on the fly.
Another thing I'm wondering about is character creation in general and aspects specifically. Veekie had a pretty solid idea for the Refresh deal on Masters and Servants, I believe.The First Adventure and guest starring phases are slightly inapplicable given that we're just two players and the "first adventure with the other PC" is the point of the plot. Using DFRPG's background/conflict/adventure might work better (though the last one can still be a linked aspect, to keep the connection part intact)?
Nasuverse magic, as we might have discussed in chat (I know I talked about it with veekie), is probably best represented as stunts for specific purposes.