The default color for annotating PDFs in Document Viewer is pale yellow. How to change this default color?
Right click on the highlighted text/object, you should get a new window with several options one of them is
Annotation Properties... Select it and you can change the color of your highlighted text.
There is no way at this time to change the default colour, you can however change the colour of a single existing annotation by right it clicking and selecting "annotation properties".
If you'd like more options you can try the okular pdf reader which has a more powerful annotation system.