Mostly I’ve just gotten used to what I’ve not liked when I’ve first started using it. After awhile, those defaults that I can’t change just become part of the procedure for me.
I agree with wishing that stroke widths, by default, would scale.
Another thing that annoys me is Adobe’s tendency to separate text-related settings into different panels. For example, in Illustrator, it’s possible to change the point size from the top bar, but not the leading. Call up the character panel, and it’s possible to change both, but if I want to change the hyphenation or text alignment, I need to call up the paragraph panel. To me, these things almost always go together and ought to be together on one panel.
Other things I just live with because it’s never worth figuring out if it’s possible to change them. For example, if I call up the layers panel (or most any panel), I probably want it to stay there until I decide to dismiss it. Yet when I go looking for it several minutes later, it’s mysteriously been deactivated.
Oh, yeah. I really dislike Photoshop’s color picker that forces me to manually input numerical values in those instances when I’d rather just adjust and pick a color from the color box. It’s hard to explain, but Illustrator’s color picker does not have this problem.
And I greatly prefer Photoshop’s simple, easy-to-use gradient tool to Illustrator’s clumsy version of the same thing. I don’t use gradients that often, but when I do, it always takes me three or four tries in Illustrator to do what I could have done in a sixth the time in Photoshop.