IMO as a Zero owner: the S ZF6 has a top speed and acceleration advantage and can carry a passenger with the $300 foot pegs option and charge more quickly with the fast charger; E+
likely has more real-world range, better brakes, better displays and logging capabilities. At this point in the Zero S lifecycle you could probably talk the dealer down $500 in price, so prices are the same.
The Zero S has two outstanding issues: an
improperly sealed BMS board which can lead to a failure when riding in rain;
motor cutouts which usually show up around 2000 to 4000 miles.
Zero has a fix for the BMS board issue and is developing one for the motor cutout issue. If you buy the Zero S verify with the dealer that the BMS board has been corrected and be aware that you will likely need to make a trip back to the dealer to correct the motor cutout issue in a month or two.
Probably there is at least a 2-3 month waiting list for the Enertia Plus, if they start delivery in a week.
Also in 3 months (Nov 15-18) the EICMA motorcycle trade show will begin. Zero revealed their 2012 lineup there last year; it's possible they may reveal the 2013 bikes there this year. The competitive landscape will no doubt change when they do so; the 2012 bikes will become discounted and you may find a discounted 2012 or the 2013 bikes to be a better deal than the E+ at that point. Note that this may mean a 6 month wait.
In any case, I would advise waiting for a short time if you don't need to buy today.