1) What exactly is the IT?
The IT is an explanation for the events in the Mass Effect game series concerning the slow process of indoctrination of Commander Shepard throughout the trilogy with a focus on the ME3 ending. It explains what is already there. There is no need for any further gameplay or cutscenes for the IT to be true. It explains the different stages of the process and how the Reapers try to trick Shepard into giving in to indoctrination.
2) Why is there only DESTROY/CONTROL available at a low EMS?
If you have a low EMS (effective military strength) you can only choose the DESTROY [if you destroyed the Collector base in ME2] in the scene with the Catalyst. Notice how the first words of the Catalyst are "Why are you here?" in this scenario instead of "Wake up" (like with a higher EMS). It could be the fact that you've spent less time near Reaper technology (reaper artifacts, indoctrinated enemies...) and that the seed of indoctrination deep within Shepard's mind hadn't enough time to develope much. You weren't able to gather a strong armada and you they won't be able to fight as long as necessary for you to wake up (you won't wake up with a low EMS), instead you die and the last pictures in your mind will be pictures of desctruction (Earth destroyed...) and as good as no hope (Normandy door opens...but you don't see anybody). However the Reapers (in this case Harbinger as the Catalyst) have no use for you anymore... so... "Why are you here?"
Another possibility is that you only have the choice of CONTROL [Collector base not destroyed in ME2]. You only have the choice of controlling the Reapers left because that is what Shepard wanted in the past, keeping the Collector base and controlling Reaper tech. You havn't rejected that choice before so this is the only thing you get now and your indoctrination is complete... No need to trick you into something else, the resisting part of you mind is obviously too weak in this scenario.
3) Why is at an average EMS only CONTROL and DESTROY available, and SYNTHESIS only at a high EMS?
First of all, if Shepard wouldn't have the option to DESTROY the Reapers Shepard would've probably seen through this illusion and rejected it. (Like in the very first version of the Matrix remember? It was too perfect but the human mind saw through it and rejected it) Destroying the Reapers was Shepard's goal right from the beginning, this choice had to be there to increase the chances of deceiving Shepard into choosing any of the other options.
By choosing CONTROL Shepard gives in to indoctrination. He will become a useful puppet to the cause of the Reapers, like Saren and
The Illusive Man. They were convinced (subtle and slowly) that DESTROYING the Reapers is wrong, (and in this case TIM) that controlling them is a real possibility and would bring more advantages than simply destroying them. TIM was obsessed with this idea (that was induced by the Reapers, remember TIM had been in contact with Reaper tech for many many years) and he was a powerful puppet that sabotaged the efforts to stop the Reapers as good as Cerberus could. In the cycle of the Protheans, their indoctrinated splinter group that wanted to control the Reapers even managed to sabotage the crucible project.
SYNTHESIS is the Reapers last ace in the hole. They know about your affection to EDI (an advanced A.I.) and the Geth (especially Legion). They know exactly what they are doing by promising you a happy future with a new DNA by merging organics with synthetics.
The only way everybody can survive (including the Reapers). Do you remember this sentence? Right, exactly the same words that Saren did as he explained his motives to Shepard -> the same Shepard that convinced Saren that he was wrong! The Reapers hope that your logic and reason will be cast aside by your emotions and that you choose to save your friends. You will be a powerful military puppet... blue eyes...remember? Blue glowing eyes (-> Saren, TIM) are not the best sign that you are on the right path
4) What are the cutscenes after you make your choice? Earth, the Mass relays, the Normandy?
As stated in this video these are the last pictures of Shepard's imagination. Depending on what the Catalyst told Shepard, you see slightly different pictures. But there is always a little bit of hope. And hope is a very important ME theme, especially in Mass Effect 3. If the Catalys tells you that you will destroy every advanced technology than this is what Shepard imagines...If the Catalyst tells you that organics and synthetics can be merged and everybody can survive than this is what Shepard imagines... These are simply pictures of Shepard's imagination.
Of course Shepard knows that his squadmates and Joker never would simply abandon him. But regardless, Shepard hopes that they will make it out alive. That they will end up on a tropical planet...somewhere save. You remember the conversations between you and your squadmates? Many talk about beaches or a tropical place... Shepard does remember... These are pictures of hope. Also notice how Joker obviously takes a look back shortly before the blast wave hits the Normandy, why would he do that? He wouldn't see anything there, it is Shepard, who hopes that they are able to escape... Shepard sees the blast wave!
5) What about the scene with the stargazer and the child?
Decide for yourself. Is it still part of his imagination? Or is this reality? A humanoid race could've found Liara's time capsules in the future, so they tell their children tales about the legendary Shepard... Or it is the actual future, where the Reapers have been defeated and those two humans are really talking about Shepard who has become a legend a long time ago. Or...it is still a part of Shepard's imagination... The IT doesn't depend on any of the possible explanations for the stargazer scene, so decide for yourself.
6) What happened to the real Anderson and Illusive Man?
We don't know. Anderson was last seen running with Shepard towards the beam. And while you were on Cronos station it is mentioned that TIM hijacked the Citadel and brought it to Earth. No more infos about their remain yet.
7) What happens after Shepard wakes up? Is the battle still going on?
We don't know what exactly is going on after Shepard wakes up, but this scene is there for a reason. It is very quiet though, so there is obviously no battle going on near Shepard. Bioware didn't provide us with more informations so we have to think for ourselves what could've happened. However for the IT there is no need for further gameplay or cutscenes to be true. Again, it explains what is already there.
8) What about the announced MASS EFFECT 3 EXTENDED CUT DLC?
The Extended Cut DLC will provide additional cutscenes and expand on the ending. It won't change it. Please take a look at the
official EXTENDED CUT DLC FAQ by Bioware:
There is no approval or disapproval of the IT. Again, the IT is an explanation that doesn't depend on any further gameplay cutscenes.
9) Did Bioware confirm the IT?
There is no official approval or disapproval of the IT by Bioware. There are however hints by Bioware employees via comments and twitters that the IT could be one of several possible explanations. But think about it, do you think Bioware will confirm it 100 % and give away that essential secret of the story or rather let the players think and discuss about the ending? Do good authors in books or movies give away the big story secrets and only allow one possible interpretation...? No... no they don't.
It was Biowares intention to think about the ending and the whole series, to create our own interpretations. Whether the players like it or not, we have to think for ourselves...
10) Does the Final Hours app debunk the IT?
No, the FINAL HOURS is a third party app for iPhone that doesn't approve or disapprove the IT. It provides you with some information about the long and complex developement process of ME3. You can be sure that they won't give away any important story secrets shortly after the game release and via this kind of media. Again, there is nothing official at all that indicates that the IT is wrong or right.
11) There are trees on the battlefield near the beam aren't there?
Yes there are trees on the far right side (if you look at Harbinger) of the battlefield and there are trees on the left side in the huge rubble piles. There are even shrubs on the higher level of the battlefield (where you start your run). But as stated in the video... there are no shrubs and no trees directly in front of the beam before you got almost hit by the laser. After this scene...there are all of the sudden lots of shrubs and even trees where there havn't been any before..
12) Is Shepard still in London or on the Citadel in the "Breath" scene.
There's a video with analysis of the 'breath' scene (which you are able to see after the credits if you have an EMS of at least 4000 and choose DESTROY) and how it's not London ruins, but parts of Citadel (watch the video here )
Remember the "illusion" is composed of many details Shepard has seen in the past. There were sure cables like that and lots of Reaper tech that Shepard saw during the last years. And there are plenty of Reaper tech in London and around the beam. There are even some similiarities with the structure around the beam and the actual crucible scene, for more comparison pictures please take a look at the following link to the BSN forum (post by byne) (Thanks to LoneIrbis for this point)