The alt-verse was *completely* irrelevant to the main plot, even going so far as to add fictional characters to the mix that didn't really serve any function (Jack's son).
Honestly, I do think that I could have written a better ending than that, provided that there actually *were* any answers to be given. (I have the slight impression that Carlton and Lindelof were just as lost with regards to many mysteries as we were, and never had any real solutions to offer.)
My take on a more dramatic, more suspenseful finale would have looked somewhat like this:
during the last few episodes of the show, everything in the prime universe suggests that the MiB is winning: he outwits or even kills main characters, to the great shock of the viewer, and even ventures to escape from the island, offering us an illustration of why it was so important to keep him on the island at any cost.
However, Desmond is the key to salvation, and all of that was part of Jacob's plan. During his trips to the alternate universe (which, in my book, would have fared much better as a real universe created by the hydrogen bomb explosion), he received a revelation that would mend BOTH universes, provided that all the key figures are brought to remember the original continuity. Once that is achieved, they fuse both universes back into one, which pretty much resuscitates the fallen heroes and banishes the Evil One, who is thwarted in the moment of his triumph. After all, Jacob's sacrifice was deliberate and premeditated (at least in *my* alternative version of the ending), all part of an elaborate strategy spanning the ages: he sacrificed a Queen to lure the MiB out into the open, and then leaves it to "them" ("they are coming") to finally finish him off.
The island *would* have mattered, and the original continuity would have been kept intact, while simultaneously allowing for dramatic plot twists that are quite unusual (such as including the death of ALL the main heroes before the finale, just to have them return by means of a fusion of universes and win after all).