Seival,
Sauruz has made many valid criticisms that I think you either failed to understand or chose not to.
It is not enough to say something could be true. If you want your theory to be valid and for people to take your theory seriously, you have to explain why your interpretation is more likely than other explanations that require fewer assumptions. As Sauruz has stated, just because it could be true doesn't mean it is true or even likely.
We do not see anyone rebuilding a relay or even the Normandy entering a mass relay. If the authors did want to portray a relay-test, these would most likely be in the sequence of scenes this thread is meant to interpret. What follows is a description of what does happen in this sequence.
After the crucible fires we see:
-A relay transmitting a red, blue, or green colored beam (depending on Shepard's choice)
-Then (same scene) the relay breaks apart and explodes as a sphere of R/B/G colored energy begins to expand outward from this same relay
-The next scene is a galaxy-map-like view of the Milky Way. In this scene, we see a dot transmit a beam of R/B/G (in a straight line) to another dot before a R/B/G circle begins to expand from the first, transmitting dot. The similarities (RBG colored beam, then RBG circle expanding) between the first and second scene listed here make the possibility that we are seeing the same thing from a different perspective most likely. Anything else could only serve to mislead the audience.
-In the same scene as scene described above, we see that the receiving dot, where the first beam stopped, do the same thing that the first dot did (shoot RBG beam in straight line to a different dot before RBG circle expands from transmitting dot). This most likely is meant to demonstrate that what we are seeing is a galaxy-map-like view of a chain reaction and these dots represent the mass relays. The beam that is being sent out by a transmitting relay causes each receiving mass relay to act in the same manner as the transmitting relay (transmitting relay sends beam to another relay before breaking apart and exploding and sending a RBG sphere expanding outward from itself). The implication is that all relays will ultimately be destroyed.
-The next scene shows Joker frantically piloting in a damaged cockpit. He looks back...
-Then the next scene shows a wave of energy with the same color and texture as the wave of energy we saw traveling 3 scenes (or about 20 seconds) ago. Another moving wave with the same color and texture as the crucible-originating wave without anything to indicate that the waves are different, of different origin, or occurring at a different time indicates that, most likely, they are the same wave. [Also, the wave is moving faster than the Normandy but has not caught up yet.]
-In this same scene, we see the a blackish, hole-ish thing begin to develop within the RBG energy wave right where the wave is closest to the Normandy. This hole continues to expand.
-Next scene a close up of Joker behaving more frantic and with a worried/frightened expression on his face. Next we see a profile view of the Normandy from a distance and, what is now a ring of RBG energy around a blackish hole-ish thing is quickly catching up to the Normandy. Next an even closer close up of Joker, whose face is appearing increasingly worried/frightened, who is also jumping and shaking in his seat as if the ride was becoming bumpy. There are flashes behind Joker that look like fire.
-Next we see a closer profile view of the Normandy as the wave of blackish hole-ish thing within a ring of RBG energy catches up to the ship. The Normandy begins to progressively waver more drastically as the wave gets progressively closer, giving the impression that the wave is causing the waver and disrupting the proper functioning of the Normandy. When the wave finally reaches the Normandy, the thruster/wings on the side facing us break off violently. There appear to be RBG lightning-like current ejecting from the wave and connecting with the Normandy, which may have caused the thruster/wing explosion/malfunction. This scene ends when a white flash appears all around the Normandy and beyond it.
Some scenes don't occur depending on what color you chose.
I think it is most likely that the crash scene is occurring during FTL travel. Relay-to-relay travel is instantaneous as specifically mentioned numerous times in the games (and, prominently, Mass Effect: Revelation) and is never contradicted (Omega-4 relay is anomalous for a variety of reason). This scene has 3 different shots of Joker doing slightly different things each one which does not occur simultaneously/instantaneously.
There is no indication that the crash occurs decades in the future despite several obvious opportunities to do so (give Joker some wrinkles/different facial hair, change the song or at least change the music).
Seival, or anybody else, if you read through this unintentionally long post, and can show me why my description and interpretation is not the most likely intention of Bioware, I would love to hear it.
Oh, and there is also a loading screen video (can't remember when it plays) that depicts the Normandy in FTL and looks remarkably similar to how the Normandy looks in the ending. If anybody would like to see it I can find and link it.