Late to this thread but it appears as if preferences for flybridges tends to break down on regional lines. Many (not all of course) that don't love flybridges seem to be in the PNW. Those that wouldn't trade them away tend to be in areas with either more clement weather year round or live in areas with 4 seasons.
Maybe it is my own regional bias, but the PNW seems to be spawning a number of the newer pilothouse designs. I am thinking of Nordic Tug, American Tug, North Pacific 38 and 43, Helmsman 38 and 42, Fathom Yachts, and I am sure some many others. These are all relatively new designs that have chosen the pilothouse design as fitting the PNW market.
As someone who hopes to purchase one of these newer designs (used of course) within the next few years, I have been very dismayed at the recent inclusion of flybridges on these designs. The NT and American Tugs are great looking boats with a useful boat deck (IMO). When a flybridge is added to those boats it detracts from the lines to my eye and because of the climate in which I cruise, seem to be a costly waste of resources. However, if there weren't plenty of folks who want a flybridge, they wouldn't be building them.
As Marin pointed out days ago, the redundancy of a flybridge simply creates something else to maintain, repair, and clean around. Around here most flybridges are fully enclosed with canvas which further ruins the lines of the boat, creates added windage, and yet more canvas for the gulls and Herons to crap on.
Some of the newer designs (Helmsman, North Pacific, Fathom) incorporated a flybridge from the first design phase and in the case of Fathom and Helmsman did a good job of keeping it low profile and minimalist. I was on a Fathom Element 43 today (in the pouring rain of course) which had a very simple helm station on the boat deck. Wheel, throttle, VHF, basic Nav display, and a small helm chair was it. I was functional and I could see it being practical for those rare times when it would be nice to drive the boat from its roof.
BTW, the Fathom Element was much nicer than I had expected. The side deck, while narrow, is functional for getting from the cockpit to the bow. The pilothouse was nice although it lacks a port side door (that bothers me). It seemed well arranged and the engine room (which I crawled into and around) was very workable.