I did conversion of about 200 pictures (no settings applied) and calculated the average time per image (QuadCore Q6600 2.4GHz, Linux, 8GB, ASP2 V2.1.2.10 32bit):
Fuji X-A1 with 16 mpixel Bayer sensor: 1.1s per image
Fuji X-E1 with 16 mpixel X-Trans sensor: 11.8s per image
So, X-Trans is 10-times slower than Bayer
(... and still some room for improvement until out-of-cam Fuji-quality is reached ...)