I like the old 1 color vector type graphics of the pip-boy. Don't think that needs any change.
But yeah, a way to mark on the pip boy map would be amazing! I love crossing off places I've been on the map. However, so far, the only way to do that is to scan the game maps included with the game guide and then print them off and have a pen handy as I explore the game. I've killed so many trees.. I don't want to kill anymore!