Whilst there are stacks of mysterious contents for later arcs that are unanswered in the OP universe, like Dr. Vegapunk, Dragon and the Revolutionary, The 4 Emperors, the Ancient Kingdom/Void Century, Will of D (which kind of relates to the former)... I dont think none of it has baffled me as much as the Florian Triangle. It was said people went missing even before Moriah, and that as Luffy and co. were leaving the Florian, Lola saw giant shadows/figures. Any thoughts on what it may be?
No idea, whatever it/they are, to be a multiplier of Thriller Bark's size, which is in turn bigger than Oars, probably makes it the largest species in the One Piece universe. Whether it comes in to valid plot fruition, or is revealed even, I wouldn't bet on it. The fact that it was subtly hinted at makes me believe it's just Oda's way of paying true homage to the air of mystery and myth that surrounds the Bermuda Triangle of which the Florian Triangle is based off .