Just spoke with Greg at WW, sounds like they've been tucking the extra brake connectors inside the downtube above the upper battery locking cradle, so that's good news!
For the couple of bikes where I have installed the brakes prior to getting the connectors dealt with (no longer an issue as noted above) I have taken a bit of silicone tape and just taped them to the brake cable. The wires follow the brake cables (contrary to claims above) so its pretty much unnoticeable. I just did the plug and not the entire wire+plug.
On the wire direction coming out of the levers, I snapped a pic on a bike yesterday. The wires follow the direction of the lines, not sticking out front like an earlier post claimed.