While I went into this expecting to hate the ending, especially since the episode "Epilogue" just a few episodes back would have made a perfect ending for the series, I was surprised by how well it worked. The show can easily be picked back up if a network wants to, and if not, there's enough closure.

As for speculation about what the writers intended to do: I read somewhere a while back they originally had a 4-6 season arc planned out, and Eli is/was one of the main characters (IMO he was THE main character) I can't believe they would kill him off at the end of Season 2. My assumption and the bet I'd put the big money on would be: 1) They intended him to either fix it and get in the pod and open S3 3 years later or 2) He finds an alternative solution to their problem before he needs to fix the pod.