Jeff, your post didn't really include spoilers. JJ didn't have anything to do with the ending of Lost though. He didn't have much to do with the series beyond its inception as far as I know.

Alias was a total write off starting from some time in Season 2. I don't know how much involvement JJ had with it at that point but it went down-hill very fast and the ending was no worse nor better than the rest of that season, let alone the few before it. That might be because I was already expecting the worst possible outcome.

How much is JJ involved with Fringe day to day? At all? That guy is attached to a ton of projects, I wouldn't be surprised if there was a machine of some sort running Fringe.