I can sorta see your point on the his suriving the car wreck but the shooting? It doesn't make sense. And I'm pretty much convinced he really is dead and that the writers just don't care anymore.
They care, or they wouldn't be writing for the show. They wouldn't be going back to little points from Season 1, etc to dig up little moments. ( Such as Dixon telling Syd how to not judge a person when it looks that they are guilty).
The shooting, is just another one of the "suspend the disbelief" moments that Alias is famous for. And in Hollywood, there is always a death scene. A scene for final goodbyes, etc. A scene with background music of Sarah McLachlan. . Its just normal. And I don't think that the moment would of had such an impact if they didn't have the scene in the hospital and just left it at the train yard.