Subsystems are explained quite well in the manual. The Weapons subst. controls aiming calculations, if you blow it up you'll notice that turrets fire awfully spread and cant hit you as often as they did.
The one that you shouldn't bust is the Comm subst. In the manual it's refered to as the "reinforcement signal", but by disabling it you dont get less fighter waves.
Hope it helps!

I can play FS1 and 2 with a mouse and keyboard without fuss.
It's not that hard to work out bindings that work for you like I did for myself. Just fiddle around in one of the training missions until you have a comfortable setup.
Venting frustrations on this board and at people who are just trying to help is not very constructive and if you simply don't like the game, don't take it out on us.

I concur with the original post, having played TIE Fighter, Freespace just... doesnt feel EPIC at all.
For example the *only* capital ship fight in the whole game is as boring as hell. I could even dive between them, stop, aim and stay there shooting the capital without fear of getting hit!
Try that in TIE if you dare....
(talking about FS1)
RANT ON:
For example in TIE, they keep you sending out with the Ties, wich can only GET SHOT TWICE (and boom you are dead), that makes adrenaline pour like you never knew before...
RANT OFF :)

This is not intended as a flame or anything, but it appears to be quite obvious that the OP is not familiar with space flight combat/sim games at all. The controls in Freespace are virtually identical to every other space flight combat/sim game of the era (and beyond, for that matter). Wing Commander, X-Wing/Tie Fighter, X-Com: Interceptor, Starlancer, etc. all had similar control schemes that are completely built around the use of a keyboard or keyboard/flight stick combo. That control scheme is intentionally designed to be complicated because these games are just as much simulators as they are games. That being said, there are space combat games that you might find preferable to Freespace, such as Darkstar One and Freelancer. Those games are much more "arcade shooter" than "flight simulator" and have controls that are much more simplified.
EDIT - Holy crap, when did I get a rep of 2? Last time I checked I was still in the negative zone...

It's supposed to be extremely easy to get rep now, congrats!

Apparently as easy as it was for me to get that negative rep. One argument in one thread was enough to drop me below the zero mark.

See, its the "intentional complication" that I quite dont agree with, especially in Space-Combat games. If you call anything in FS2 worth of a "Simulation".. then I gotta say its as unrealistic as it gets - having to constantly thrust to keep your velocity in Space? But thats ok, a game should primary focus on beeing enjoyable.
What quite killed FS2 for me is that it seems to be a great game, just manically overloaded with redundant options (and thus controls) that mightve seemed like a good idea but are useless once you think about them.. (Tell me one sane reason why you`d want to switch Missile->Missile->Torpedo if you loaded 3 slots instead of simply Missile->Torpedo)
Some ppl on this board (cogadh: Not you, even if I quoted your post) act like I planned to throw out 10$ so I can bitch on the forum.
Negative Rep here I come =)

See, I think that's where the problem lies. People do find this game enjoyable... mostly the kind of people who also enjoy complicated sim games. I think that, perhaps, you are not that kind of person, hence why you didn't enjoy the game. I do agree that the physics of the game could have been more realistic (they were actually pretty good at the time), but I hope you weren't trying to thrust your way through the game by holding down the "A" key. There are keys that set 0, 1/3, 2/3 and full throttle as well as keys that increase or decrease the constant throttle by 5%.
Those seemingly redundant controls do become somewhat less redundant when you add a flight stick to the control scheme. Since my flight stick has throttle controls and more buttons than I can count, I end up only using the energy manipulation and messaging keys on the keyboard, while the stick handles all of the flight and combat operations. I actually find the game's controls to be somewhat simplistic at that point, in comparison to some of the other space flight combat/sim games I have played. I remember having games that came with keyboard overlays that you needed an engineering degree to make sense of.
As for the weapon linking, honestly, I never noticed it as an issue, probably because I haven't found a point where I actually needed a torpedo (yet). From what you describe, I do agree, it would have made more sense to allow individual weapon selection to go along with the ability to link particular weapons together.

yeah.. like I said before, I find the game annoying as well, to the point where I can't even get past the tutorial missions, it's just that I don't care to break out my flight stick, I never really used it, and I don't really want to blow the dust off for one game.. plus it's not really my type of game..

Freespace is not "intentionally complicated". The controls are designed to give the player as many options as possible.
Stuff like shield and energy management as well as all the targeting controls seem pointless at first, but as you get better at the game they're usefulness become more apparent. Mastering their use is almost a requirement at higher difficulties, multiplayer, and more difficult fan-made campaigns.
A lot of the functions in Freespace don't seem useful to a beginner the same way some kids can't grasp why turn signals are useful in a car. It's only when you get better at the game that their usefulness becomes more obvious.
For example:
Beginner's bombing run against a destroyer.
Go full throttle at the destroyer until within range and bombs lock onto target, then sit still next to it launching bombs until target is dead.
My bombing run against destroyer:
Cut power to primary weapons and divert power to shields and engines. Target nearest weapon on destroyer. Approach full throttle until within range while maximizing forward shields as necessary and rear shields as well if there are enemy fighters approaching from behind. When within range, gain weapons lock and continue approach until within 500 meters of target weapon before launching bomb to mimimize the chance of the bomb being shot down. Equalize shields and apply afterburner to gain distance from the destroyer. Repeat until target is dead.
(this is just how I do it, some others might employ somewhat different methods depending on how they play.)