I like to keep my crazy wiring 'hidden' so to speak.. Have the guitar look stock but then keep one or 2 little secrets 'under the hood'..
1) This one I'm doing on a LP style guitar I'm in the process of dreaming up.. Stock 2 humbucker, 3-way switch, 2 volume, 2 tone layout with 4 options for each humbucker: 1) series, 2) parallel, 3) north coil split, 4) south coil split.. Add the fact that you can have both humbuckers in parallel courtesy of the 3-way switch, and you've got a whole bunch of selections on a stock looking ax..
2) I've always wanted to have an little indicator, like a small light or LED, which would change colours for each pickup selection.. Dunno, just thought it'll be cool..