I prefer to run my soffits first. The main reason for this is I don't use a level for siding. I pull a line off each corner of the house. Sometimes the fascia is ran out of level or has irregularities in it. If I run the soffits first I can fix this and then when I pull my string it's perfect.
I also will never will trap the siding behind the soffit.
A good example of why is one of the projects we are on now. Cedar shingle ran all the way up, then they nailed a cedar 1x6 freeze over it, then they screwed aluminum j-channel to the 1x6 freeze.
Since we are only replacing the siding, we are having to cut all the cedar at the bottom of the 1x6 freeze otherwise all the soffits come down with it.