There is already two minor forms of these skill features in game: buff and chemspray. Done well, they can make a huge difference, but most players prefer the simplicity of the reactive tools.
The other issue is that a good engineer is rarely idle: they are either fixing something, firing a gun, buffing/chemming, or they are keeping any eye on arcs that the pilot/gunners might miss. The last may sound unimportant... until your balloon dies to an unseen carrofish. A good engineer keeps their eyes open, and glances about as they preform their duties; a single unspotted ship can ruin an entire team's push. .
Hey, didn't they have a galleon? Where'd it go? *engines exploding* oh, there it is!
As it is, there are times when three engineers can't keep the ship running, much less two. (On a squid: captain brought moonshine, tar, claw. Used scroll wheel; was forgetful.) Even on the "simple" ships, such as the goldfish, a well organized crew can bring buff/chem, and keep busy with those.
As for the skill involvement, in my mind it comes down to knowing what to repair, when to do so, and how best to get there. AI may be better on some ships, but there's a reason AI engineered mobulas are rare. Learning the optimal routes, and when you may need to leave your post to make it before the armor break, can be the difference between a healthy ship and a smoking wreck.
The guns are similarly divided between those the AI can use well, and those it cannot. I've never seen an AI gunned munker, and while I can't be sure (having not seen one), I doubt it would be effective. Loosing special ammos means that a decent human can always outperform the AI, even if it's only getting in a few extra shots by starting with lesmok. Others benefit from timing/context: as anyone teaching new players how to run a metamydian knows: "hold until red!". At long ranges, some rely on predicting where it will be, which is again easier for humans then AI.
To summarize: there is a lot of skill involved in engineering and gunning, but it is a learned, knowledge based skill rather then quick reflexes arcade-style skill.