I've always thought that the Derelict(errm, Juggernaut when alive and in working order apparently) was essentially the carcass of the ship, having "died" some time ago decaying to the overall look of it that we see in the film(Alien). When I imagined a "Live" Derelict it's funny how close Prometheus captures what I envisioned.
I've always thought that the Space Jockey's were a biomechanical race and obviously, that would naturally extend into their technology. I always pictured their tech as a strange mix of bio-organic material meshing with biological and metallic mechanical devices.
In the case of the Juggernaut ship, over time the metal would degrade to show what we see in Alien, the Jockey himself having grown into the chair and everything becoming skeletal due to the passage of time and the ship "dying". Whereas in Prometheus, everything is "Alive" and in pristine operating condition.
The way I see it, is that the Juggernaut in Prometheus is in pristine, un-battered, "alive", and in proper operating condition whereas what we seen in Alien is the carcass. That is assuming this is the same ship(I personally think the movie is more of a prequel than they are saying, but that the concepts it presents are larger, or grew larger than simply Facehugger(orwhatever might've caused the SJ to be bursted)-->Attack Space Jockey ---> Space Jockey emergency lands on LV-426 --->Roll Credits.
And that Ridley and Co, while still wanting to do the prequel and explore the mythos a bit while also trying to do something a bit new, thus the concept evolved somewhere just past a simple prequel to Alien. It evolved into Prequel To Alien Plus.
I do recall reading an interview where Ridley pretty much said the same thing that I did(Juggernaut in Prometheus = New and Alive, Derelict in Alien = Mostly dead Carcass of said ship).
