[Japo]

My two cents...

1. I guess so, but in my experience you can't possibly walk into an alien's line of sigh withuot getting shot, no matter your soldier's reaction rating.
2. Each combination of weapon and shot (snap, auto, aimed, etc.) has an accuracy percentage as described in the UFOpaedia. If I remember right you must apply that percentage to the soldiers' accuracy rating and you'll get your base hit chance, which will display when you click on a weapon to select the shot. That figure is what you should pay attention to. (For example 90% [snap with heavy plasma] of 68% [a given soldier's accuracy] is 61%. A soldier's accuracy rating can be above 100 as high as 120 per cent.) I guess it could be modified because of distance, but when I had good marksmen so that their nett percentages were over 100 per cent for aimed or even snap shot, they hit even distant aliens without ever failing.
3. Different weapons may very well make a different, depending not on the weapon itself but on the excess damage done besides the damage necessary to take the UFO down. Al least the manual states that if you assault an UFO that has landed on its own instead of been taken down, you'll find more booty --and more aliens.
4. I thought it should depend on the weapon and your attack stance (cautious, standard, aggresive). Or maybe the damage you deal depends on the damage taken by your craft, and an Avenger is way sturdier than an Interceptor. Or maybe it depends on the craft itself as you say if you've observed it isolating other factors, I don't know.
5. Of course there's a limit you must respect, but you decide which items to carry. In the base go to "equip" the transport craft and decide what's in and what's out, you'll be told about the limit. Then when already on the battleground you'll of course get to decide what each soldier carries in each hand etc.
6. It may be innate, look in the manual. (If you have so many doubts about advanced topics you really should check the manual.)
7. I don't think so, just build an hyperwave decoder and hunt down UFOs on Alien Retaliation missions as if your life depended on it --it does.
8. I'm pretty sure it's destroyed and the game tells you about it.
9. As I said just hunt down retaliating UFOs... I'm not sure at all but, as stupid as it may sound, I think that each retaliating UFO has to find you separately. This doesn't mean that it won't happen several times, I think they search around the areas where your craft have been active.
10. I think it is for them just like it is for your team. So they only need to know where your soldier is, but the alien with line of sight is not the only one who can mind attach him, all the rest can as well. Also they're pretty good at it and at figuring which of your soldiers is the mentally weakest.
11. Consult the UFOpaedia on which weapons are most effective against which aliens.