Good Evening. I like the ideas here. How about a sidebar that pops up with priority boxes to control engineer behavior? What is a priority box, you ask? The most recent example might be Dragon age, where you control tactics with a priority box system. Another example would be the gambit system of final fantasy 12.
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[1] [ repair engines -->]
[2] [ repair defensive structures-->]
[3] [repair starships-->]
[4] and so on....
On the right column, we have selectable boxes (denoted by the arrow). I only mention these other games so as to give precedent for the success of the system in a popular title, consumed by the masses.
I don't like the idea of specialized units because it quickly becomes messy trying to maintain one of this, one of that, three of those, and so on.
I
do like the idea of being able to configure behavior. I wouldn't worry about confusing your audience. This is, by nature, a cerebral game- I think we can handle checkboxes or some sort of configurator.