Based on the eyeball test three of the theories, that appear to be getting the most support, relate to either Life Model Decoys, a super soldier program or magic relating to the Scarlet Witch. The Scarlet Witch has already been announced as one of the characters that will be in The Age of Ultron movie.
In the first episode agent Hill and a doctor discussed that Coulson did not really know what happened to him and that for some unknown reason he should not learn about what happened. Based on those two criteria I do not believe that the LMD fits the storyline surrounding Coulson.
One of Coulson’s great appeal is that he appears to be a person of great character and humanity. In simple terms he is just a good guy. A LMD would cheapen that perception. He would just be a android which could be programed. Why couldn't he be told this? A wishful theory of many fans is that Coulson is the Vision. The Vision was fully aware that he was an artificial lifeform. I think his humanity is too important to replace him with a robot.
The theory that is based on magic is supported by the reference to Coulson’s musically talented girlfriend that some speculate could be the Scarlet Witch. Additionally, during the first two Shield episodes Coulson indicated he was sent to Tahiti to recover. When he mentions Tahiti he always talks about it being a magical place.I believe that the word “magical” is a misdirection. Also I don't see why someone could not be told that they died and were brought back to life. Emergency doctors do this somewhat regularly. Also, using magic to resurrect someone would cheapen future deaths. Just roll out the witch and problem solved.
At this point my favorite theory relates to a hybrid of the super soldier formula. The obvious question is why can't he be told what happened. I will get to that a little later. I believe the super soldier theory can pull support from several places. In the Hulk movie Blonsky was given a formula similar to Captain America’s formula. After the Hulk crushed him against the tree it was first thought he was basically going to be crippled. The formula kicked in and Blonsky was healed. This delayed effect would explain that Coulson did die. It would not cheapen the movie either. Fury might have truly thought Coulson died prior to the formula “resurrecting” his body.
Additional support to the super soldier formula came in the first episode of the show when Coulson did the Neo Matrix back bend to avoid the van door.
So back to the issue of why can't he be told the truth. Captain America knows his past. The answer lies in the fact that every formula, other than Captain America’s formula, has major flaws. If they worked perfectly S.H.I.E.L.D would have an army of super soldiers. My theory is that the formula (my actual theory relies more on a tech based nanobot reprograming of the brain rather than a chemical compound) did work on Coulson, but only for a short period of time. The formula reversed itself and left only slight benefits which would explain his Matrix move. The residual healing factor might not have been even known by S.H.I.E.L.D until after he died.
So why can't he be told. Simple, when the formula reversed itself Coulson basically lost his memories. S.H.I.E.L.D has always operated on the edge of ethics. I believe that through some type of memory implanting (I like a tech based implant) they took advantage of the situation and replaced his memories to create a perfect agent. It can be foreseen that his family was informed that he was killed in the service of his country.
His response that Tahiti as a magical place is purely an automatic response to his updated programing. I dont even think he was ever in Tahiti but he needed to think that his healing took a long period of time. Coulson even referred to a short time during his death that he saw a white light that could have been part of the memory implant process. The unexpected healing aspects could not have been explained other than by telling him about the failed program which erased his life and allowed S.H.I.E.L.D to reprogram him.
I believe my twist would not cheapen the Avengers movie. Fury truly believed he was dead and the motivational factor that helped draw the team together would not be based on a falsehood (other than the Ketchup on the Captain America cards). Coulson would not be cheapened. He was always a good man but he has just been reprogrammed as a different good man. A man who does not have a family and can devote his whole life to the agency. Coulson’s man-crush on Captain America would be supported by the fact that he volunteered for an updated program. Steve Rogers was chosen because he was a good man and I believe the same was true for Coulson.
If the show finds long term success a side story could involve Coulson’s origins and the life he lost.