When the pin obscures the text, it slows down our reviews; so I'd love a change, too.
WHAT OTHERS ARE DOING:
Adobe Acrobat's method is easy to read: when adding a comment, they put a sticky-note icon (equivalent to CC's pin) on the user-selected location, then the text box is to the side, with a yellow line leading to the sticky-note icon. They still have the weakness of obscuring the doc with the icon, but they allow you to zoom-in, and the icon stays the same size while the doc grows bigger (so that eventually you can see the obscured part).
I've seen other PDF editors that create a text ballon when you click, with an arrow to the point first-clicked. The text ballon is moveable.
IDEAS:
Pin-Arrow: I think an improvement over Acrobat's method would be for Code Collaborator to make a yellow arrow from the pin to the use-selected location, and then the pin could go anywhere. I'd recommend that the yellow arrow be color inverting, so it will still show up in case it is being placed onto a yellow document. Perhaps this pin-arrow concept could be made such that the first click sets the arrow head, and the second click sets the pin location. Extra points if they can be dragged after placement (I know, now I'm pushing it!).
Arrow as New Artifact: Let me be extravagant for a moment -- but it might actually be easier to implement: Keep the current functionality with the pins. But then allow users to add yellow arrows anywhere, that don't have to be tracked. This feature would allow me to put my pin in an empty margin, then draw an arrow from it to the location of interest. Additionally, I could draw multiple arrows from one pin to several identical targets (e.g. "this item needs wheels in the following locations", or "you missed a period in these three sentences"). Maybe the arrow tail always comes from the pin automatically, or maybe you just let them free-draw it like in Paint or Visio or Word....
Just some ideas...