With so many pairs you have the possibility of investigating more profoundly the structure, like if the difference $y_B - y_A$ depends on the "starting point" $y_A$!
You could fit a model like $$ y_B=\mu+\text{offset}(y_A) +\Delta (y_A-\bar{y}_A) $$ and you could even add a quadratic term $+\Delta_2 (y_A-\bar{y}_A)^2$ or you could replace the linear+quadratic term with a spline using a generalized additive model.
Graphically you could show the lines as you have shown, with a reduced alpha factor (*), maybe reducing further by only showing a random sample of lines. Then you could color the lines according to slope ...
(*) alpha factor here is a graphical parameter making points in the plot transparent, so the first plotted points is not totally occulted by later overplotting.