In 4.0.34-beta we've reduced the hit detection, which was unnecessarily large, and made the shear tool indicator slightly smaller and more translucent. Hopefully that helps a bit.
Unfortunately we don't have a way to change the size of the tool indicators. They are always drawn at the size of their graphics, so they look crisp.
Have you tried deselecting (spacebar, escape, or double click) so you can more easily make a new selection?
You could set a key for the Hide Selection hotkey, which hides the tool indicator and everything else normally drawn on top of your images (bones, everything), but only when you have a selection. That can help if the tool indicator is in the way visually, but you'll still need to deselect to make a new selection.
