It would be nice if 100% accurate navigation and continuous accurate projection of own ship position on the map would be optional.
Give us a sextant!
You wouldn't have to use it personaly if you're not so inclined. But you could tell your crew, say through a set of standing orders to use it at regular times.
Let the map not show an accurate postion, but a projected, approximate position from your last known position. Not having 100% accurate navigation would add another dimention to this game. A good navigation officer would realy make a difference.
It would also be nice if you, or your crew, would be able to navigate visualy using landmarks. Let's say you're near a coastline. On -any- good sea chart, there's tons of info on easily recognisable landmarks to navigate by (I should know, I used to do it). Landmarks aren't neccisarly just building, but terrain features that stand out as well.
Take a bearing of two (or more) landmarks and where the lines meet, that's where you were at time x (when you took the bearings). Could be similar to my Manual plot post. Instead of a target mark, have nave mark button. And let the crew draw the position on the map.
As with my manual plot suggestion: the more accurate your reading, the more accurate the crew can draw plot your position on the map.