Seems to me that a lot of this could be remedied by looking at the map, manually pointing your ship in the direction you need to go and hitting the throttle.
After all, we can't expect these Ensigns straight out of the Academy to know how to do everything. Sulu forgot to disengage the parking brake on his first time out.
All of my BOffs are Commander-rank.
Also, that's not 100 percent. Not only is it difficult, and very hard to do with any precision, it's also purely 2d. At least with Autofly, there's a CHANCE you'll get the right height. Autofly also stops you when you get close enough to enter, which means you can grab a soda and not worry about flying a sector block away in the mean time.