Comparing electrics is basically down to comparing MSRP and various incentives if applicable.
If you use city/highway range, the Empulse gets 77 miles from 9.3 kWh nominal battery capacity (142 Wh/mile @ 85% charge efficiency) and the Zero S ZF8.5 gets 70 miles from (probably) 7.6 kWh nominal battery capacity (127 Wh/mile @ 85% charge efficiency).
At $0.115/kWh, this represents a cost of $0.0163/mile Empulse and $0.0146/mile Zero.
The $0.0017/mile charging difference adds up to $170 over 100k miles. Pretty negligible in the grand scheme of things.
I think the Zero S ZF8.5 and the Empulse non-R are the most comparable of the two bikes. The ZF11.4 offers (in theory) significantly higher range than the Empulse (21% higher mixed, 25% higher highway) and the Empulse R is much better at being a sportbike.
IET and appearance IMO are subjective. The Empulse's IET should give it a small advantage in acceleration and top speed .. the bigger advantage would be if you specifically wanted the ability to shift gears. Riding both may be a good plan if you're on the fence.
Empulse non-R pros:
* faster AC charging (22 combined miles/hour vs 8.8 miles/hour Zero)
* 5-20% more range than ZF8.5
* probably more consistent performance, range due to liquid-cooled motor and battery cell heaters
* larger motor controller
* nicer brakes & suspension, sportier tires
* chain drive is more durable
Zero S ZF8.5 and ZF11.4 pros:
* ~10% more efficient, per range specification
* belt drive is very quiet, maintenance-free
* smartphone integration
* integrated storage (tank, charging cord)
Zero S ZF8.5 pros (vs Empulse non-R):
* faster DC charging (67 combined miles/hour), with optional CHAdeMO upgrade ($$)
* much lighter (350 pounds vs 470 pounds)
* $3000 lower MSRP
Zero S ZF11.4 pros (vs Empulse non-R):
* faster DC charging (88 combined miles/hour), with optional CHAdeMO upgrade ($$)
* 13-25% more range than Empulse
* lighter (382 pounds vs 470 pounds)
* $1000 lower MSRP
Edit: added a Zero S ZF11.4 comparison
