I am not sure I see the advantage of a 650B option. The 700 C tires larger diameter provides better, more efficient rolling and the stock 45c wide tires seem plenty wide for commuting purposes. If you really need a wider more comfortable tire, the RipCurrent S is an option. As far as puncture resistance goes, tire liners are a cheap and easy add on, but you can always swap out to the tire of your choice.
You mention a derailer upgrade, this was actually an option when the CCS first launched along with a 10 spd cassette. Must not have been very popular because I see no mention of it now.
The chain retention problem, however, should be addressed. I would like to see an inner guide on the front chainring, or a chain guide stock. I know Reid has taken a few links out of his chain which eliminate chain drops. I am guessing the bike ships with a full length chain capable of accomodating the 56T front chainring option. Appropriate chain length definitely improves shifting performance as well.
As for the fork option, it seems to me a longer travel fork is counterproductive in a commuter bike. If you are really planning on lots of gravel or bumpy riding, again the RipCurrent is a better option.
The upgraded brakes would be nice as an option, as well as the seatpost.