So far I have played through 3 times| 86% 1st go 99% 2nd and in my third now at 99%.

Things i missed in first 2 plays:
-Never calibrated all the towers (couldn't be bothered too annoying)
-Only got the Choco Eater as the culprit in the Mi'ihen Machina Mystery
-Never completed the "Here comes the bride"* or Publicity Campaign side quests.
-Never raised any Chocobos above level 2 or found any items or dungeons.
-Did not complete the puzzle cave in Thunder Plains at Chapter 5.
-Lotsa other stuff >.>

So what am I missing?