What I mean is, if I'm at lvl 85 and at the start of the entire storyline, are there parts of the story that are time-sensitive (like, gotta be there while it's happening in a given patch)? Or is MoP basically sequenced via phasing, like WotLK and Cata?
One thing I'll note is that 5.1's story requires you to do dailies to progress through it's story, and 5.2's story on the Isle of Thunder takes place after it and relies on a very critical event that happens in the latter parts of 5.1's story, so from a sheer story perspective, get exaulted and finish the story with Operation: Shieldwall or Domination Offensive depending on your faction before doing Isle of Thunder.
As posted above, 5.3 but it's mostly a teaser for 5.4 and not a whole lot of lore you you'll miss out on, especially if you're alliance.
Oh, and the storyline with the Golden Lotus daily chain, but the only important parts in it are building up towards the thunder king's return in 5.2.