I think Fuji have a bit of a marketing nightmare on their hands.
X-Pro2 is rightly the flagship in the sense that it has the hybrid viewfinder and with AF updates and a new sensor its going to be a great camera. However a lot of people (rightly or wrongly its still a fact) prefer the SLR shape and the additional control provided by an ISO dial etc. I think Fuji realize that they have a huge audience for the X-T its been there most popular camera and that if they wait to long to release it after the X-Pro2 then they might annoy everyone.
They obviously want a little bit of time for the X-Pro2 to be the only game in town so it does not get totally trounced in sales which would be embarassing given its the 'flagship' model, and more expensive.