AJ Styles is one of those guys like Jericho or Benoit was in WWE in the early/mid 2000s. By that, I mean he's able to jump back and forth from the the main event level to the midcard (in WWE lingo, it would be World Title picture to Intercontinental picture) pretty easily. The main problem (like braveh said) is that AJ hasn't gotten back to the main event scene since Hogan & Bischoff decided they wanted RVD to defeat him for the title (soon after their arrival in TNA).
When Hogan & Bischoff first arrived in TNA, I think they were willing to give AJ a shot. After all, he was the Champion when they first came and he was playing a babyface at that time. Although it was soon after Hogan & Bischoff's arrival that they paired AJ with Flair & turned him heel. It seemed their plan was to make AJ the new "Nature Boy", but AJ just wasn't suited for that. I suppose Eric & Hulk thought that AJ wasn't "big" enough to be Champ on his own, so they felt like they needed to insert Flair into AJ's title reign.
I think that when Eric & Hulk first arrived in TNA, they were like "AJ who?"...so they decided to try and make him more "marketable" (or whatever) by pairing him with Flair. Even though they didn't think AJ was a big enough star to be the TNA WHC at the time of their arrival, I hope they see things a little differently now that they've been with the company for a little while. During AJ's last title run, I remember there was a match on Impact between Angle (the challenger) and AJ (the Champion). This was when AJ was still a babyface; before he was paired with Flair. I think it's possible the match happened during TNA's brief run on Monday nights as well, but I can't remember for sure. AJ won the contest (obviously, since it was RVD that eventually beat him for the WHC), and after the match Hogan appeared on the entrance ramp and said something to the effect of "those two [Angle & Styles] are the best professional wrestlers in the business today" (or something like that). Hogan (and Eric too, probably) may have thought that AJ was one of the best wrestlers in the business, but he obviously didn't care much for his character and/or gimmick...since they tried to make him the next "Nature Boy" soon after that (that may have even happened at the very next PPV, I can't remember for sure).
Either way, AJ eventually went back to being AJ (the character he was before Hogan & Bischoff's TNA debut). I don't know if that happened because of his split with Flair, or if AJ just told management that he didn't want to play the "Nature Boy" character anymore, or why exactly he went back to his old gimmick. It could have also been that TNA creative realized that AJ wasn't cut out to be the new "Nature Boy" as well. AJ has bounced in & out of the main event scene ever since, but TNA creative doesn't seem to think of him as the main eventer he once was.
For most of 2012, AJ has been involved in the storyline with Kaz & Daniels (as far as I remember). Every time he got close to the main event level, Kaz and Daniels were there to make sure they screwed it up for him (cost him matches, etc). There was also the whole Maury Povich thing they did, where they were saying that AJ was the father of Clair Lynch's baby, etc.
Now that AJ's involvement with Kaz & Daniels is over, it looks like he's going to start yet another feud with Angle. Maybe TNA creative is thinking that if they put AJ in another high-octane feud with Angle, he'll be able to look like a main eventer again (at least in the their eyes). At least I'm hoping that's what they're doing with AJ right now, I think they've only kept him away from the main event scene lately because it had been so crowded (especially since they elevated Aries to the Main Event this year as well).
To answer your question (finally, after that ridiculous amount of crap above - lol), I think that AJ will have at least one more run with the TNA WHC. I'd bet that he will get the title at some point in 2013 (at least I hope he does), and maybe again in 2014/15. As someone pointed out earlier, AJ pretty much is "the" TNA guy (he's basically their Cena, except without the "superhero" gimmick) - and the company would be silly to not put their title on him again (especially sometime in the near future).