Jacob and the MiB didn't even appear until the Finale of Season 5. If the first 5 seasons were "building up" to the clash between the two, with Jacob's name thrown in here and there, then it's safe to assume that you want that build up explained. If you don't explain it, then the first 5 seasons were just filler material, and filler material is crap and pointless. You could have just opened at the beggining of Season 5, then had the big clash between these two demigods.
Walt and Annie are not the only two. In any case, let me address your counter argument for the Walt problem.
The creators of Lost admitted during the filming of the first season that they'd have to make 6 series to make their money back. That's always been known. The creators, (Abrams et al) know how long it takes to make a Season, and understand that networks like to leave big gaps between airing them. So why, with all their knowledge of TV production, would they build up a child actor into a major part, knowing full well the duration of filming would likely span across years, and that those years would have an obvious effect on that child actor? It was irresponsible at best, shortsighted at worse. I don;t believe they "accidentally" didn't take into account that the child would age, that would be enormously stupid and not something that could be attributed to the type of people that are creating this show. They're not stupid, if anything they've had a very clear idea of where they're going the entire time.
Which leaves the only other option, that they never intended to resolve Walt's story. They've already backtracked on Annie and The Volcano, why wouldn't they back track on this?
Thus, they're not going to tie up some important pinnacles of the plot.
I'm not saying it's a bad show. I'm merely saying that they've purposefully created important plot elements with the sole intention of keeping people watching and filling up network air time, with no intention of following them up. They're not just little bits here and there that could be attributed to "back story" like Adam and Eve, or why Desmond is "immune" to the rules of time travel (in Faradays words) or things like that. Walt was a major plot subject throughout the whole of Series 2, not some half-arsed character with issues mentioned on the back of some other unexplained mystery.