sorry was a tad late answering, lets get to it:
Guns - eh Full rack of PRG is usually the idea. If you are rolling in enough money by now, and the ships can fit them, pulsed beam emitters are awesome for ai - virtually no flight time on the projectile means it hits rather often. If your computer is having staggering issues in combat (slideshow stuff) then its performance degrades however.
Factories - If nobody is buying a ware, nobody buys it.. end of :p Equipment docks act as a 'sink' for weapons, shields, and missiles however - you can always SELL any type of those to an equipment dock, where it dissapears forever.
Jumpdrives - its a ship extension sold at home of light (terracorp, again), or in .. legends home (otas), or at.. One of those boron systems in the south east (another hq building). Terrans sell them, but only after you finish their plot.
It jumps you to any *gate* that you have enough e-cells to get to, cost being 5/sector for fighter, 10/sector for freighter(i think) and 20/sector anything bigger. Any units following you with a jumpdrive and enough e-cells will make the jump as well. Yay micromanagment.
'help' I believe if you convo a carrier of some sort or other military craft and ask for help *and if they have no other orders* they might help you. Maybe.
I'm usually too busy blowing stuff up..
convoy escorts - ... uh. Pelican is a TM, right? It has hangars.. If a unit is set to protect, it will launch and pewpew stuff that attacks the leader. I would .. er ... Ignore this option - generally out of sector fighting gets your ships killed.
Complex construction.. heh. If you have two factories, you can connect them with a 3rd factory 'complex construction kit'. Basically you build it the same way, but you select your two factories and then place a 'hub', where stuff docks at. They essentially become the same factory with multiple production lines..
Wingmen - The best stance for AI wingmen is 'dock at nearest station'. (maybe youve noticed,..) If Protect me only works AFTER you get HIT. Otherwise, attack my target might work better. Protect me works once you have a carrier of some sort that is both incredibly slow and crappy at dodging shots..
@velox: Yeah, its an awesome game.. If you get past the fact that the autopilot is suicidal... *sigh* its as good as can be expected really. Anything better and it becomed hellova cpu drag.. More than it already is..
Missile defense? huh? oh.. Believe it or not, usually the focus of a hostile attack, even with multiple ships, is you. You are the aggressor, and they focus on you.. Your wingmen usually are busy shooting stuff and colliding with stations to be annoying really. Anyway - The hostiles are shooting you, not your wingmen. So thye dont have a problem with missiles.. And when the turret is set to 'none', that literally means 'sit there uselessly'. You need fight 1&2 for missile defense i believe
Astronauts.. heh. Bring them to your local pirate station. GO to your command console, under piracy? and select enslave passengers or something. THen sell them as slaves.
MARS is nice and all, and I quite swear by it, but its annoying as hell when your trying to pod-board hostile ships. missiles are COMPLETELY USELESS against a target with mars+goblins. Its annoying as hell. Thus, I had to turn it off for the ai.. poor things...
Yeah, a lot of the game is balanced around the stage from fighter -> m7. Largely a player in an m7 is 'the endgame', as .. well, strafe... *sigh* Unfortunately, the strafe drive is also the only thing that lets the player compete beyond his level - I once, mistakenly, let the AI have beam weapons. Instant-hit, beam weapons. Thus, ... ... ... strafe drive was useless suddenly. So.. well.. it wasnt worth it. It was balanced so that fighters could still work fine..ish, but capship engagements were quite literally 'who had the bigger stick'.... Generally not fun. Ever since then, I have campaigned against beam weapons in any form in the AI's hands...
Anyway, minor tangent.
Its an awesome game, sure its got a flaw or 5, but the scripting and modding team really make up for it. <3 them