no one ever came back from the dead.
Sayid was dead.
They also never said no time travel
They did. I posted the quote here maybe a month ago. It went something like "there are no spaceships, there is no time travel". They were reassuring people that everything on the island is normal and "based on science" (another quote that does exist). Granted, they were only talking about what had already happened up to that point, but I still think it's an indication that they had very, very little idea of what was coming, otherwise they wouldn't have made statements like that.
I don't think they were left with a "mess," they were left with a rough plan and then worked out how to make it a reality. Things only really cemented after year 3 when they inked out a deal with ABC to end the show in year 6.
But they were still left with the task of explaining a bunch of things that were clearly throw into the first season without an explanation in mind, like the whispers the jungle (intended to be a sound effect for the others at first, except they turned out to be normal people) or Smokey himself (he sounds like a heavy monster on the first episodes).
