As much as I hope it is the indoctrination theory, I can come up with some "Bioware-Quality" answers to some of the points I believe:
-Destroy is Red, Control is Blue:
Simply put, Destroy destroys the Reapers, yes, but it also Destroys EDI and the Geth, as well as any other synthetics out there. Killing your friends and possibly allies to destroy the Reapers is what Cerberus was doing - though it was killing its people to try and control the Reapers - and thus is represented as the Red option: You destroy the Reapers and all the Biological information they hold about the earlier species, you destroy an entire species - they Geth - themselves, and you destroy your friend and, to an extent, saviour: EDI.
Control is blue as it saves everyone and everything. The Reapers still exist, but are under Shepards control. As such, they stop harvesting Organic life, start defending it, and can help rebuild the Mass Relays. In addition, the Citadel is still intact, so the seat of Galactic power still exists for people to live on, and for the Council to govern from. We can assume it is also controlled by Shepard. From there, everyone lives. The biological data of the Species from previous cycles stored within the Reapers survives, the Geth survive, EDI survives. It offers a great chance for the galaxy to rebuild, with everyone maintaining their individuality, but still surviving. In addition, it has the best watch dog fleet to stop trouble from ruining it.
-The "One more Story" line must hint towards after end DLC:
Not necessarily. After that scene, you are told that you can now continue to build on Shepard's legend by continuing to play through the game, and through DLC. What that line implies is basically that the Stargazer tells another story about one of the other missions Shepard went on, so that as you finish up anything you hadn't done before attacking Cronos Station, it is merely the Stargazer telling another story and building on the legend of 'The Shepard'.
-Can someone write a script and ruin it completely in the last 5 minutes:
Yes, if rushed. I believe there was another planned ending, something to do with Dark Matter, but for some reason that didn't go ahead and they shoved this stuff in to work with what they already had and finish the game on time. Don't know what happened there, but I will hunt down and kill whoever forced the script change.
Also note that in DA2, whilst a different group - same publisher, Leliana lived no matter whether you killed her in DA:O, and rather than admit it was a bug, they said that it was perfectly intended that way and that the player didn't necessarily know, but she survived that incident. Even though you decapitated her.
-The child seems to be merely a manifestation of Shepard's fears or W/E, and thus that whole last section is likely in his head:
Whilst the child may be purely in his head (I fully agree with this), the child being in the final section is likely either his perception of the Catalyst, or how the Catalyst chooses to present itself to him.
-The Citadel exploded and Crashed to Earth or W/E, Shepard couldn't have survived that:
An unknown device fired a beam of energy that magically disintegrated all Reapers/Synthesised all Organics with Synthetics (Control is more understandable, but why the Relays blow up in it is beyond me) - Your argument is invalid.