Answer #1 : Yes I can definitely see an improvement in image quality over the X-Pro1. It helps to have a well developed eye to spot the differences.
Answer #2 : If you can only buy one lens to pair with the X-Pro2, get the XF35mm F1.4 R. It's sharp, colourful with plenty of contrast...and cheap.
Answer #3 : The best lens for single subject portraits is the XF90mm F2 R LM WR. The XF56mm F/1.2 R is a very close second.
Answer #4 : Yes...it's better than the X-T1, however the X-Pro2 is a "rangefinder" style, while the X-T1 mimics a standard DSLR.
NOTE: With a single exception, all images were processed in Adobe Lightroom/Photoshop CC using the Fujifilm Acros Film Simulation profile.
Personally I feel that if you want the best quality images to compare then use the software that comes with Fujifilm cameras (Silkypix). It takes a bit more effort than Adobe Lightroom CC and is not equally versatile but it renders X-Trans files much better.
SAMPLE X-PRO2 RAW FILE [DOWNLOAD] *** Available For A Limited Time ***
XF35mm F/1.4 R (1st Generation Model) W/Speedlite mixed with window light
XF14mm F/2.8 R - Long Exposure W/Tripod
XF35mm F1.4 R (1st Generation Model) W/Modelling light from a studio strobe
XF56mm F/1.2 R W/Light from a desk lap
XF60mm F/2.4 R Macro W/Silver Reflector & White Bounce Card
XF60mm F/2.4 R Macro - Natural Light
XF90mm F2 R LM WR - W/Studio Strobe & Silver Reflector
XF90mm F2 R LM WR - W/Studio Strobe