Maybe other information regarding these lens can be useful in deciding. So, I would say:
XF90mm:
Good points
- WR
- Fast and precise AF
- More magnification (2x more than the XF56mm)
Weak point
- Needs more working space for portraits
XF56mm:
Good points
- Smaller and lighter
- More versatile
- Low light capability
Weak point
- AF in low light
So, running subjects (kids and pets) in the yard with raining possibilities, I would go for the 90mm.
Indoor portraits, more static subjects and better all-around possibilities, I would buy the 56mm.
I think this site makes a fair analysis:
http://toolsandtoys.net/reviews/a-review-of-the-fuji-xf-56mm-f1-2-xf-90mm-f2-0-lenses/
Some photo comparison here:
http://www.cameralabs.com/reviews/Fujifilm_Fujinon_XF_90mm_f2_R_LM_WR/verdict.shtml