Given the lineage of the show, I'm not surprised that Jacob and the MIB weren't necessarily fully fleshed out concepts from the start. That's sort of the problem with most TV Shows anyhow. Someone has an idea, that person's idea turns into the show, others (Darlton) create the story out of that idea. I think we're getting better (see: Mad Men, Breaking Bad), but some things are simply out of people's control (networks' wishes, where they came in at, etc.). It's not like Damon and Carlton sat down, wrote drafts of the entire series, and then started making it, like an author would, but neither have they "been making it up episode by episode, season by season" either. It's always been pretty clear that the Others S1-3 are a little off in comparison to what we see now.
That being said, I'm relatively trusting of Darlton in that they've had a clear path for the ending since S2 and it isn't something that was thrown together in this past year. The framework has been there since S2/3, if the finale fails to deliver, I'm not blaming it on "making up shit on the fly".