Obviously, the Zero has to be bigger. I accept that (sort of). But I prefer the Arduino/Photon layout for 2 main reasons:
a. The GPIO pins straddle the breadboard halves. Very handy. No stiff ribbon cable required.
b. Instead of the side mount, the micro USB points out the end so a compact enclosure (e.g., hand-held) setup is possible. As is, the minimum inside width of a Pi Zero case is 2.5".
Here's my layout plan:
Note that I've left off the 2nd USB and HDMI plugs. They could be added via a daughter board connected through the above "accessories" slot. For the daughter board I'd provide a full-sized HDMI and 2 USBs.
Re: living with current reality— Anyone know of a compact/right angle micro USB plug?