Personally I would rather see a waypoint system simular to Tribes Ascend then a marker on the minimap.
In that game it would place this 2d marker on the spot where the enemy is seen, so that you would have an icon pop op the screen, showing the location.
Think building healthbar, but then the icon of the spotted alien, visible from everywhere on the map (shows though walls).
Minimap idea
Re: Minimap idea
le mi'a bende cu nitcu lo zbasu