This sounds odd, but look at your shifter adjustment.
On my ST, when I switched from my warmer weather boots to my cooler weather boots which have taller instep and toe boxes I was having to really jack my foot all around and way down with the toes for upshifts. Next outing I wore the warm weather boots to avoid the clumsy shifting. The upshifts remained as clumsy with those boots as with the winter boots.
So I played with the adjuster and eventually set the toe lever to the best "higher" height. Shifting up or down is now perfect. Funny it took almost 2 years to discover that I needed to adjust the shifter position - especially since I switch back and forth between bikes constantly which should have made the clumsy position more noticeable much earlier.
BTW, this is the first bike I have ever seen with the shift linkage rod having right hand threads on both ends. Its nice in that it makes it impossible for the rod to unscrew itself and drop the center section on the road somewhere. But to adjust it one either has to disconnect one of the ball joints, or pull the shifter off the pivot and rotate the whole thing.