Greg, I hope not. While I like the idea as a design matter, I don't think that it's a code issue.
Along those lines ... I'd like to see some of the anticipated changes being the topic of threads in the "2008 NEC" section. Or, am I the only one who bothers?
As to the paddle fan, it matters not which colored wire goes where, or which switch is closest to the door - at least not from a code perspective. Of course 'black to black' looks neater.
When you are using a cable-based wiring method, I really like to bring the neutral to the switch. I like to do this because it makes troubleshooting later, and because we're seeing more lighting controls that require a neutral. With cable as your method, you can't just pull in another wire.
That ceiling box can get pretty cluttered, pretty quick. While this isn't a factor when there is but one switch .... make it a 3-way with travellers passing through, and it gets crowded. For 3-way loops I prefer, if I'm running cable, to NOT pass through the ceiling box. Again, pipe is different; you can pass different colored wires through, without splices.