My friend had a pretty good idea, after getting frustrated trying to select clones from a whole bunch moving in opposite directions.
There should be an option that when clones are overlapped, left clicking will select a left facing clone, and right clicking will select a right facing clone.
If you left click and no left facing clone is under your cursor, it should select a right facing one anyway (so we can still left click to pick out clones that aren't in groups and don't have to think about which button to click all the time).
It might be nice, as I don't really use the right mouse button anyway, preferring to edge scroll or use tab and click to move the camera.