Depends on where you boat and how you use your boat. We never run our boat from the upper helm. Neither I nor my wife like the sight picture from up there as far as operating the boat is concerned--- we feel much more connected to the boat from the lower helm and find it much easier to judge close-in maneuvers like docking from the lower helm than from up above. Plus we can hear and smell what's going on in the engine room and electronics consol, something that most likely prevented a fire several years ago.
We boat year round and in the winter the flying bridge is not somewhere one wants to be unless it's enclosed and heated.
But if one boated in a warmer climate and liked the sight picture from up top, the chances are they would run the boat all the time from up there so a lower helm would be of little value. The big sportfishermen did away with them altogether quite awhile ago.
Personally, my favorite boat configuration is the pilothouse--- Krogen, Victory Tug, De Fever, Fleming, etc. The pilothouse gives you some elevation if you like that but it's out of the weather. Plus many pilothouse designs incorporate a flying bridge if you like the option of driving in the open when the weather permits.