| Map Layers|
Often I've found it annoying that certain explorable areas do not appear on the main map due to being underground, with the mission map sometimes being displayed there when you're in one of them. The idea of map "layers" would make these areas seem more accessible, and also allow for many towns and outposts to be located underground (and even beneath other areas). The Sunspear Sanctuary just looks out of place where it is.
Basically, in the main map view, you would have the options to view different maps at different depths that correspond to one another spatially. Now the main problem with this is that dungeons and such areas are not always to scale with the above ground area they are meant to stretch across. A good excuse for this is that (unless the Guild Wars world is flat) the deeper you go underground, the smaller the area around the core of the planet is, so depending on the scale of the planet, that could determine the depth of many of the caverns.
Another problem is that it could be very frustrating to have to flick through many layers of the world just to find the map you need, so a better option might be to have "window" cut-outs from the ground level map revealing the dungeons beneath, that you can switch on or off, or have them appear when you put your mouse over that area.
The same system could be applied to underwater and possibly sky/floating regions.
Update: Also, with this system, you could have explorable areas stretching across above and below-ground regions, instead of needing to separate them.