The smoke monster will be fully explained according to Lindelof.
About the pirate ship I think it has already explained in an internet 'game' they made some years ago. Plus there's nothing to really explain IMO. It's possibly just a pirate ship that crashed years ago in the island.
The time travels they introduced in the fifth season can and will explain a lot of things. For example the role of Widmore (remember the episode with Locke?), about Danielle Roussaeu and her crew, etc.
One of the things they never talked about is the statue foot. Well they mentioned in the fifth season, which means they didn't forget it.
One more proof that they know what they're doing is that in some episodes you go back in an incident that happened some episodes ago and watch some extra time of it.
I refuse to believe that they just decide to change something and then rebuilt the whole set, clothing, etc, just to shoot some more extra seconds.
The more recent example is
They have already shoot it, but decided to show it some epuisodes later. That's a proof that they have everything in mind.