A possible realization: was Michael's 'afterlife' not in the limbo of the FST because he was trapped on the island? I always wondered why it was randomly Michael who appeared in Everyone Loves Hugo, and why he didn't appear in the FST on the plane. The FST and the whispers may be seperate entities, but what if those who were trapped on the island for what they did, like Michael, weren't able to ever exist in the FST? Perhaps those who didn't deserve to 'move on' stay stuck on the island, unable to go back to the FST and move on with the group?
That could explain the missing people in the church reunion: Michael (and therefore Walt), Nikki, Paulo, and Eko weren't in the FST because they should've been stuck on the island as whisperers because of the sins and murders they committed, therefore never moving on in the FST. (That and the fact that everyone hated Nikki and Paulo, and the actor who portrays Eko asked for 4 times the amount of money he was offered) That also might tie into why the characters with the most questionable moral complex, such as Ben and Ana-Lucia, weren't ready to move on yet; they still had the chance to redeem themselves in the FST before moving on.
So, is it really FST vs. whispers? Comment as you want, obviously the ending was somewhat ambiguous and oepn-ended. I only ask for no comments about 'how bad the ending was', there are other blog posts for that.