I think adding waypoints to Missions would be a vital asset for Star Trek Online.
I know myself I got lost a few times in missions on where to go, where things are, etc. For example the last mission 'The Doomsday Device' I had to charge up torpedoes at a plaents core. I was like what... how would I do that... I started flying around until I saw a medium sized plents tore to bits and figures hey thats where I probably need to go. I have this problem numerous times during missions.
Waypoints would be very helpful. Especially when you open the area map... so you have a idea of what areas of space you need to visit... and plan strategically.