I hope JJ & crew have a really good idea where the show is going. There have already been a couple of questionable episodes here and there, but nothing X-Bad. The other thing to hope for is that the creative minds keeping things on track don't get bored when side-lining on other projects. If you'd like to see how bad this can make a show, look at Alias. Easily one of the worst shows on TV this past season (ok, it wasn't as bad as Threshold). In 13 short episodes they managed to undo anything positive about the past 4 seasons as well as create more plot flaws and character flaws than pretty much every other show on TV combined.
Every now and then I find out about some random plot point or episode theme for Lost. It doesn't bother me and I certainly don't go looking for it. I'd rather keep the show "in the box." They're definitely taking some notes from Twin Peaks, but it'll never be the same calibre of work.
Bruno