My reason is just as kcdgg points out.. also IF there is ever any other electrical problem it is easier to pin point if the stock wiring is used. Although... I do not practice what I preach. I don't have a JB, Stock Ignigtor, Coils, or Stock Wiring Harness. In fact I don't think I have a single piece of the original electrical system on my bike. The pick-up coils are aftermarket, as with the headlight, ignition switch, starter, turn signals, tail/brake light, gauges. I think the only three pieces of stock electrical parts on my bike are the temp sensor, fan switch and the fuel sending unit. I am racking my brain and can't think of any part of the electrical system that I haven't touched and upgraded to my needs.
Now I know my system isn't for every one... so I show the easy no brainer way to wire the Shidegen R/R in such a way that even a "Campbell" (the most incompetent mechanic I have ever run a crossed) can hook it up with out any hick-ups and every thing works as its supposed to... Besides, I also like a nice clean wiring harness. and having a piece of the harness dangling for no reason drives me nuts. So my OCD kicks in and I have to trace out all the "unused" wires and cut them out of the system.