Aside from the issue of Art´s job, which a lot of us think won´t come into play until later on, i think the season will end up putting in place 2 issues for next season:
Boyd-Dixie Mafia: regardless of what happens with Ava, he is getting into a seriously precarious position with the mafia. I think these plot issues have been obviously laid out during the season while the Drew mystery played out.
I think it goes beyond Boyd at this point. Tonin and the Detroit Syndicate (which IIRC is separate group from the Dixie Mafia folk, as far as Duffy and the Dixie Mafia being beholden to Tonen the same way Boyd and his family were beholden to the Dixie Mafia types) are hanging over everyone and I would be shocked if they are the new big bad that will hover over the series these last two seasons.
Tim-Colton: if Tim ends up putting him down (which may be a bit of a given, i dont think Colton will survive the season, since ep 1), there is no way it is going to be simple or clean. Rachel or Art or Raylan may know something is up, or even be there to see it (i can see Tim not giving a shit if Raylan is there). i don´t think they can have Tim fully deal with the issue in 3 eps to go. So the real fall-out may be left for next season.
BUT, if they gave him [Tim] a storyline this season just to kill him off? I will cut something.
I think Tim could be dead man walking; not just because of the sudden storyline they are granting him, but because it would create something for Rachel (wanting to avenge Tim, perhaps pursuing Colton and looking for the perfect moment to kill him in cold blood) and because it would create an even bigger shitstorm between Raylan and Boyd to explain away why the two men would be blood enemies, in terms of Raylan knowing that by sparing Boyd in the pilot, he set into motion Colton coming to Harlan and killing Tim as part of Boyd's criminal enterprise, which would never of existed if Raylan put Boyd six feet under.
I don't really get the Limehouse as "banker" thing. What service does he provide? He doesn't launder money or pay interest. He isn't trustworthy, witness him "changing the terms" of the hostage deal. Seems much more trouble than he's worth. How many local criminals have enough money that they need such a "bank"? If he hides money in pig carcasses heck I'll take my chances and hide my own money out in the woods under a rock thanks.
Hiding it in the woods can be riskier; putting your cash with Limehouse, who lives in a section of the county few dare to enter, seems like a safer bet. Especially if you are a criminal in Harlan and can't hide your money in other ways that would be available if you were in a big city and had money men laundering it for you.