Uhm I think the alternate timeline is the "magic box" sort of. Basically, it's what the characters deserve - I mean, remember smokey asking Sayid if he would join him if Smokey could give him what he wanted most (ie. Nadia). And then in the alt timeline, bam, that happens.

I'm also thinking that the Island sunk b/c Smokey left it, which is why everyone is freaking out about him leaving.

Either that or the writers really just have no idea. I think that might be it.