Well, one obvious one is.... if the map view is at an angle (i.e, not looking straight down), will map markers be obscured if they're in valleys behind mountains? In which case you'll need to rotate the map around to see certain things. (And how much does rotating & zooming mess with the whole "recognize the areas of the map, which way is N/S/E/W, and which direction you need to go" thing)
Another question is how fast the transition is between First Person view -> looking at map -> back to First Person. (Which might or might not matter, depending on the feel. I know some people have complained that pulling up the pipboy in FO3 was too slow for them, whereas I didn't have a problem with it because it fit the setting.)
rotating a 3d map of an area wouldnt mess with my ability to find my way. there would likely be a compass showing directions and it would make finding something with landmarks much easier than looking at a paper map. i.e "oh i need to go to a place between two gigantic rocks about 3 miles NW of this city. lets check our GPS map and see where i have to go. *maps out what looks like 3 miles in a northwesternly direction* oh hey. look. two gigantic rocks. ill head that way." a GPS map would make navigation multitudes easier especially if youre lost simply because you can see landmarks. what landmarks are there on a paper map? if youre lucky they will show a forest. you likely wont get terrain or elevation.
i honestly cannot see any drawbacks to the GPS map. in my opinion it makes navigation easier.