The XE-3has improved AF and the sensor uses dual conversion-gain technology
Both these improvements make a difference in low light. At least I noticed a difference with my X-Pro 2.
Dual conversion-gain sensor technology is also used in all FUJIFILM bodies with XTrans III sensors, many newer SONY bodies (incluing the APS-C 6300) and the D-850.
If you aren't interested in low-light scenes, the the XE-2 would be more cost effective.