For me, the two things I really like about the RPi (and BBB) are that I can plug in a full size keyboard and display, and that I can write and edit programs on the thing itself. Or I can use SSH or Remote Desktop, but I'm still programming directly on the target device.
I need the ergonomics of a full sized human interface due to my advancing old age, but I just have a visceral dislike for cross programming environments, where you program in an IDE on one computer, and run your program on another. Maybe this goes back to my earliest experiences with computers, where you flipped a switch (or entered a user name) and were instantly greeted with the BASIC prompt. I put up with cross development for microcontrollers, but still prefer a direct route.
Also, I'm not afraid to kill the RPi, and I can start over from a completely blank slate if I want to. When I think that I've gotten something working, I often wipe the system and re-install everything to make sure I know what would be required if someone else wanted to use my program.
As for my "case," I just attach everything to a piece of scrap plywood with wood screws, in the original sense of the "breadboard."