Lisa never died. The plot of the game was not a dream. The Others took advantage of Elliot's amnesia to make him believe he had been responsible for Lisa's death. Elliot was drugged and taken by The Others to implant this suggestion, in order to be able to manipulate him into helping them get Jack. Her appearances throughout the game on the island were really her. The plot of the game was a hint from the creators that all the "ghost" characters we have seen so far (including Jack's father and Hurley's meeting with Charlie) will be explained without supernatural/dream explanations. When he was sent back in time, things were slightly different, and this time he met Lisa immediately, so The Others will not be able to manipulate him this time: thus he becomes one of the background characters without a significant role in the plot.
But Lisa was alive this time, suggesting a change in the time line or an alternate time line.
The writers stated that they do not believe in alternate time line or changes in time.
In season 6, an alternative time line is introduced, so it's possible that Via Domus is a 3rd time line
Of course, the game is non-canon, so some liberties may have been taken with the time travel mechanics from the series- after all, they don't come into play until the end.
The game serves as a substantial glimpse into the unique properties involving travel to & from the Island. As we learned with Desmond, when experiencing time-transported consciousness (TTC), the Island has its' way of bringing you back. This could be indicative of what we can expect to learn about the Island from the coming episodes of the show.
After his exposure in the Swan, it would be possible that on his leaving the island, Elliott was "transported" back to the moment of the crash, hence why he "lost" his memory.
However, this would put Elliot in the predicament of also needing to find his own constant.
Also, he did not exhibit any of the more severe signs that Desmond and Minkowski showed when experiencing their TTC; confusion, aggression, black-outs, bloody nose.
It is possible that Elliott was thrown from the continuity of the game into the continuity of the show thanks to the effects of the time-travel.
Elliott is led by the compass, which is controlled by The Island, on a path of self-discovery and ultimately makes him recognize his biggest flaw, and change his ways. As a reward for learning his lesson, The Island leads him on a path that will cause a time paradox that changes the past to bring Lisa Gellhorn back to life - his true "way home". The smoke does come face to face with Elliot, and chooses not to kill him, but instead forces him to continue on his path by blocking his way back.
The compass was placed there by Ben, Writers do not believe in Time Paradox and the Island cannot bring someone back alive. How could the island bring someone back to life if they died and the body remains outside the Island. The only person who is possibly alive is Christian Shepherd, he died outside the island, but his body is in the island.
The idea of a time loop that is affected by the character's decisions each time through the loop is prominent in Stephen King's The Dark Tower, which has been referenced in Lost more than once before.
The entire experience is a dream given to Elliot by the island to see if he is worthy of being alive in the island, but must first pass a test. The island created events using survivors and placed him in situations similar to those of his flashbacks (lies and betrayal).
All events shown in the game are in fact a dream of sorts (possibly caused by the Island) that occurs while Elliot is still unconscious after the crash (he imagined the whole thing, with flashbacks partially based on his memory).
The events that occurred in the flashback did occur except when Elliot told the guard she was a reporter resulting in her death. This is something that he was planning to do but didn't; which would explain why she was in the crash at the end and his attitude during the flight of not having any sense of guilt of her being killed.
The manifestation of Locke was his guide as he made Elliot find the compass and secured a boat to the way home; something to note is that in the game Locke is on the pier when in the show, Locke should have been inside the Swan during the Swan Implosion.
The event causing the sky to turn purple wasn't in fact the swan implosion but Desmond's almost failed attempt to type in the numbers into the computer which caused the crash of flight 815 as seen in the cutscene.
The "Locke" we saw at the end (and maybe on several more occasions) was in fact the Monster.
The ending should only be seen as a little surprise by the game producers to spice up the gaming experience at the end (since it would have been quite boring if it had really ended the supposed way). Due to the lack of creativity and production/development time they used a time loop which however doesn't fit into the concrete plot ideas of Cuse and Lindelof but still leaves a mystery to solve - **This would now fit with the game due to the current theme of season five involving time travel/loops**. Would also fit into the various plot errors which were brought on throughout the game.
When leaving the Island, Elliot's present consciousness jumped back in time to some point where he could stop Lisa from dying but still get on Flight 815. A fluke caused Lisa to survive the crash, despite the likeliness of course-correction.
Suppose the series is about a group of people in a virtual reality simulation, in which all of them are successful in real-life and the simulation is their fantasies of being losers shipwrecked on an island. When you die in the simulation, that’s just the person being disconnected. The simulation is sometimes rebooted, which is why events repeat. This would explain the ending: Elliott "reboots", and this time, Lisa is involved in the simulation.
When Elliot saw "the plane" crash, it was not his plane. The electromagnetism, along with other island forces, or just being out-of-sight, Elliot was the only one who saw this plane crash. He might have drove his boat over there. And it might have turned out that Lisa never died in the first place. She was shot, but perhaps doctors were able to save her. Savo took her onto another plane, which is the one that crashed, also the crash that Elliot witnessed. When Elliot arrived at the crash, only Savo and Lisa were still alive. Lisa had lost some of her memory, she only forgot what happened at Hotel Persephone. Therefore, Lisa trusted Elliot. They took the boat home. LATER, they survived another crash, the one shown at the end. The whole game is from Elliot's point of view. So in this crash, Elliot loses some, not all, of his memory. He can't remember anything since he was leaving on the boat.
Non-Canon Status Explained
The simple reason as to why the game is non-canon is because all but the last half-minute of the game is not in the same timeline as the show. This explains why the following happened:
Michael was already building the raft on Day 2.
Jack went to the Black Rock with Elliot sometime in season 2 time.
The Flame has the Swanlogo on its door because the Swan logo was originally the generic DHARMA logo. Supported by the fact that Pierre Chang is wearing a Swan jacket in the Arrow orientation. ("Because You Left")