With the longer/heavier lenses I prefer to use the XT-2. I don't have the 16-55 f/2.8 but I do have the 100-400, which is Fuji's largest, and recently I bought the 80mm f/2.8 macro (also heavy). My reason for using heavy glass on the XT-2 is because I normally have the vertical battery grip installed, this balances much better with the large lenses. Also, the extra shutter release button for vertical shooting is ergonomically better in every way.
None of these reasons matter for the smaller lenses which is why they are better suited to the X-Pro2, both aesthetically and ergonomically. There are some lenses that work on both cameras such as the 16mm f/1.4, 23mm f/1.4 and 56mm f/1.2, and you often see an X-Pro2 combined with these.
But if I didn't have the vertical battery grip for the X-T2, the difference wouldn't be so clear. Having said that, I am happy using my right eye for the X-Pro2 and the left eye for the X-T2. If you have a strong eye preference either way, use that to guide you as well.