My thoughts:
1. Really, this will vary by the situation. Laser, basic, and mlrs are all popular choices. Missile are good as well. Don't put sniper turrets anywhere near your wormholes, they are better for shooting from afar. Spider turrets can be great for slowing down enemy ships from great range.
2. It really varies. You don't have to unlock any defensive techs, but depending on your playstyle you might prefer some versus others. People prefer harvester exo-force-fields if they are getting their resources raided a lot. Mark II force fields if you are losing a lot of command stations. Mobile Repair Stations are great for taking with you on raids to keep your fleet running tip-top. Transports are a must in some situations where you want to bypass permamines or planets with a powerful ion cannon. But other techs are also useful, in a variety of different situations. You seem to be looking for an ideal build order, and there is not one -- you have to make different decisions based on the map and scenario you are playing.
3. Pretty much answered by 2.
4. Yes, they have to kill the enemy, and then you get it if you aren't already at the cap for that type of enemy, and if you have enough energy to support it. And supposing that the enemy is not "immune to reclamation" in its abilities. Most of the smaller enemy ships will be converted.
5. Most likely don't worry about it. Probably stray mines, or else stray remains rebuilders or similar. In the latest prereleases, the extra engineers and remains rebuilders will go elsewhere to stop bugging you with the count of extra cloaked ships, though.
6. Ha -- opinions on that vary widely, you won't get a straight answer from the group on that. Also, it depends on your scenario. Unless you are playing against a lot of cloaked ships, tachyon beam emitters are pointless, for instance. But against cloaked ships, those are invaluable. I think most people agree that the advanced warp sensor is basically just for newbies. And, that armored missiles are almost never useful, though they are in some really really specific circumstances. Oh, and EMP mines aren't very popular. Other than that, I think somebody likes most everything, but it varies by circumstance.
7. Yes, but that's only for when you have excess metal/crystal after having already built everything else. In other words, if you're at ship cap already and have a bunch of cash flowing in that you otherwise can't use, spend it on mercenaries! Otherwise, they are too expensive to be worthwhile; the overflow-cash scenario is what their purpose is.
8. Yes, it only shows stuff that is actually in the current game. The full list is much longer.
9. Hold shift, and then give the orders. So hold shift, and then right-click all the destinations you want on the galaxy map or on the current planet, for instance. You can't give move orders to a ship on a planet it is not already at, though -- to make incoming ships gather at a certain location when they enter planets, you want to unlock and use a Rally Post (DEF category).
10. To get your ships out of your transport, there is an unload button. I think there is a hotkey for that, also, but you have to hover over the button for it to tell you. Might be U, I forget. Your ships will also safely disembark if the transport dies, so no worries there.
11. The Control Nodes have a variety of functions. You'll have to read the in-game text to see what each one does, but it should be pretty clear. Mainly they affect the global behavior of some of your ships. If you're new, there's no need to worry with those just yet, but they do provide some opportunities to fine-tune your ship behaviors.
