first off let me say welcome to the game and the forums,
2 you get used to the camera controls or at least i did.
3 i never use strafe and i get along just fine without it
4 when your IN combat and not on the map there are a play and pause icon on the left side or at least i think there are these light up accordingly.
5 dont ever play windowed mode.
6 no way to speed up the game you're meant to take an active part not stand by.
7 compared to the other missions that one is "easy" difficulty does not scale the AI it scales the odds from what i can tell number of ships and what type on either side.
8 i find the best way to beat the first mission (haven't done it in awhile myself) is to have everyone stick together, light escort the cruiser with the fighters and manually pilot the destroyer close by.
9 restarting the game almost always fixes the autofire bug you described never had it happen more than once to me. and trust me autofire makes combat WAYYYYY less frustrating i can't imagine having to constantly switch to my pd weapons and manually target missiles, well i can and it sucks. EDIT i just looked at your bug report post as well, the flashing light on autofire means it on but you have control of the weapons selected so it won't do anything unless your off them for example if you set you PD lasers on group 3 to autofire but manually select it it will do nothing, try selecting your main guns or your missiles. and as well the weapons must be in range of a target such as a missile or an enemy to actually fire otherwise it would waste ammo/flux.
10 the reason the destroyer didn't respond to orders the first time is because it was YOUR flagship you cant give yourself orders unless its on autopilot, your meant to always be ingame with your ships, autopilot is more so you can take a drink while your ship crosses the vast emptiness of the combat field.
11 i suggest you try the campaign its the "New game" button on the main menu it will better prepare you for the missions i myself have beat very few of them with a good score. but just so you know you shift click or shift ckick and drag the mouse to buy less than 500 of something it will come in handy trust me.
the tutorials are great for the basic of the basics but the campaign will prepare you the most, you'll be able to learn what ships do what without sitting and staring at the codex for hours, although it definitely helps that it's there.
Finally again welcome to the community i hope you enjoy your stay, and remember its only in alpha its not even beta!
btw under options there is a setting that is basically easy mode and normal mode its the half or full dmg setting at half you only take half of the incoming damage on full you take the normal amount of damage.