Yep, he [Khawaja] is a complicated case. He was very unlucky to be dropped in Sri Lanka - he had the spot for his first extended run in Tests, but Ponting got injured so Marsh came in, and of course Marsh made a ton to hold his place for a while after that while Khawaja was left out. He came back in against South Africa but he was only there as an injury replacement for Marsh, and this is where he actually looked his best. Against New Zealand he looked horrible though and he was scapegoated a bit for the drawn series, dropped for the series against India (where he probably would've actually scored runs tbf).
All in all he was pretty unlucky throughout all that and I think the selectors would even admit that, but he's not been at all unlucky since. He averaged under 20 in the Shield for the rest of the season after being dropped and didn't cross 50 once, then had a fairly meagre stint with Derbyshire averaging 40 odd with one hundred in Division 2, and when Quiney was named as Watson's replacement he'd only passed 50 twice during the summer without converting on either occasion. He's picked up a MOTM award and scored a ton since which are good signs, but the way he handled being dropped he had no right coming back into the side, no matter how unlucky he was initially.
I think the selectors and most of the fans are thinking that the top three in Tests long term will be Warner-Hughes-Khawaja, but they all definitely have some work to do on their techniques before it becomes a reality, particularly the latter two. Hughes's problems have been well publicised but I actually think he has a better technique than Khawaja as it stands despite obviously being less orthodox and less aesthetically pleasing. The real downer for Khawaja is just how easy it is to bowl to a plan to him; if you pitch it up outside off you'll not only get him fishing in defence but completely tie him down as well. This is in contrast to Hughes who has a great strength right next to his weakness, so if you try to get him caught slip and you don't execute quite right he will murder you square on the off side; you actually have to tuck him up to tie him down which is unlikely to get him out. Being able to punish the bowlers when they err in their typical plans is what effective batting is all about, and Hughes does that so much better than Khawaja at the moment, who at Test level just isn't really going to get waist high balls on his body to pull away all that often.