Normally, I pick based on what is better or easier for each aspect of the job. There really isn't one choice that is universal. If you are stick building a shed, I am pretty sure nails are the best approach for all framing work in terms of speed and productivity. For other stuff, it can probably go either way. In terms of speed, I can probably put in 10-15 well placed nails with a framing gun in the time it takes to drive one equivalent screw.
Thinking back to the last shed I built, the entire floor frame was nailed together with my framing gun, and plywood decking was nailed on with the framing gun. Wall framing was definitely all nails, and nails for the sheathing/siding. All nails for roof framing, and nails to put roof sheathing on. I know I used lots of screws too, but can't really remember where....
For some stairs I built that go down a 40' bank to my dock, I used mostly bolts and screws to put up the framing and beams. Then framing gun with nails (glue-coated ring shank) were used to nail the stringers onto the side frame, and to put all the stair treads and risers on. Railing posts attached with bolts, and then railings were nailed on.
For my boathouse roof, more screws were used than typical, but I did use the framing gun and nails to laminate 2x lumber into beams, with some bolts in key places. Roof framing was nailed together (rafters prefabbed into trusses before being lifted up into place). Purlins were put on with impact driver and star drive screws, mainly because I wanted the pull-out capacity for uplift resistance, and got better numbers with two screws per purlin/rafter intersection. It was also a lot easier working with an impact gun and screws up on that roof hanging over water than wrestling with nail gun and hose. I can put an impact gun in a holster on my belt. The nail gun would probably pull my pants down if there was even a way to hang it from my belt. One big change on this project was use of Simpson structural screws for hurricane ties and other structural hardware. I used hanger nails where I could, but in many places the structural screw was easier to use.