Let's be honest here, there is still light ahead of the tunnel IMO.
Watson - should be moved back down the order, I mean he's not an opener originally unlike Rogers and Hughes. Probably can still have a role in the side as at least he can bowl and can make starts, but he's clearly done little with the bat since the 2010/11 Ashes.
Rogers - an interesting case. Old, but has dominated domestic cricket in the past. Looks sometimes solid but has had a knack of getting out to poor deliveries. A series by series basis, if he fails here then move towards someone else.
Khawaja - deserves to be the #3, he needs a fair go at Test cricket to see whether he sinks or swim.
Hughes - should open, it's what he's done for most of his career. Otherwise, give him at #6 a go. If he struggles there, then discard him.
Clarke - obviously keep. Only batsman who's worth his weight in piss. Will be mighty annoyed if he retires.
Smith - shows balls at least. Keep him in the side, plus he can occasionally bowl well.
Warner - isn't even scoring runs for Australia A. Needs some big scores to get back in the side, but has more natural talent than most which I suppose is a good start.
Cowan - he's 31, never dominated Shield cricket and has been mediocre. I know he's a decent, intelligent bloke, but he really isn't test match material. Would never had gotten anywhere in stronger times.
I think that Top 6 should remain our top 6 for the near future, with Warner coming in for Rogers sometime within the next 12 months or if some of our other batsmen still can't hack test cricket. Many of these guys are young, done well at Shield level, and some of them show fight, so our batting stocks could be worse. Things should go up within time.
We have other problems, but none nearly as concerning as our batting.