The change of IntRect and FlipX/Y are not really comparable, since IntRect was changed, because of its more logical use x,y,width,height while not affecting the performance in calculating the 'third' information (instead of x2-x1 = width you now get x1+widht = x2).
FlipX/Y on the other hand was removed to clean-up the API and remove redundant functionalities. Since one can simply set a negative scale factor to flip a sprite and the scale function gets implemented anyway, the FlipX/Y just aren't needed anymore.
Arguing about simplicity of FlipX/Y vs. scale with negative factor isn't very strong, since both ways have the same simplicity to use.
The only argument I see as valid, is that FlipX/Y would be more descriptive than the scale function. But I happily take a cleaner API over a small bit of readability.