My most recent commuter bike is definitely not so clean as Adrian's. To a certain extent it's quite difficult to craft minimalist e-bikes, as the very things that tend to make them fun and useful (batteries and motors) also tend to occupy a fair bit of space.
I went for a form-follows-function approach:
I tried to keep it all very clean and organized. The controller is mounted to the underside of the rear rack (about 0,5cm from the tire) and camouflaged by the wire baskets which flank it, and the wiring to/from it is all contained within a piece of inner-tube which keeps it neat, organized, and out of sight. The control wires which need to cross from the rear to the front do so inside the battery bag, and follow the contours of the bike's native brake and shifter cables. Not much can be done about the motor cable, so I just tried to give it a nice graceful curve.
But at the end of the day, there's just no getting around the fact that the battery itself is quite large. If I'd been willing to spend several thousand dollars more, I probably could have had a custom frame created which housed the individual cells inside the structural tubes of the bike itself, but I feel that placing the battery where I did is an acceptable compromise for my bike in the same way that a lot of people seem to feel that purchasing front wheel drive cars is an acceptable compromise for their automotive needs.
The concept of "average" requires that 50% of the population be below it.