This game would be so much better if you could pay for engineer mods and you didn't have to travel to each engineer.
The fun would come in experimenting with the right mix of mods for your ship and play style.
Finally, it would be great if there were missions that could only be completed with a very clever mix of engineer mods.
One of the main points of a game where you fly a spaceship is that you get to fly a spaceship. Given this, I don't understand the complaint of the game making you fly your spaceship to do things...
More and varied missions would be welcome, though.