Someone mentioned on twitter that it was shown out of order. Apparently it was supposed to be shown earlier in the season. That would have made more sense. But yes, it would have worked better as interspersed scenes.
I wonder if that was a wishful-thinking tweet. This episode aired when planned, according to Alan Sepinwall's interview with Damon and Carlton:
[Q:]Even some people who were positive about the episode last night objected to or questioned its placement this late in the season, right after this big episode where so many characters died and right before the final hours. And at times I and other people have wondered about whether Desmond should have more prominently appeared in the sideways universe sooner, or if we needed to spend as much time in the Temple as we did, etc. Looking back over the season now, how do you feel about how you placed things and about certain landmarks. Did they have to be at the particular parts of the season where they occured?
CC: We told the story the way we wanted to. Like David Chase, we tried to make the show to entertain the audience. That was our primary goal. We kind of planned this episode to come at this period of time because we actually wanted to take a break after the deaths of these major characters. It felt like this was the perfect time to take a time out from the main narrative. And since this was the final big mythological episode that we were going to do, we felt like it was a good placement for it, and now we'll roll into the finale. We make no apologies. We planned this to be the way it is. Again, it is funny, because there are a lot of people who are very happy with the show, there's going to be a very vocal group of people who are not happy, and that just kind of comes with the territory. We're making the show the best way we know how to make it, and we stand by it, and we're excited about how it ends and how the journey's unfolded.