It looks like the wishes of Star Trek Director JJ Abrams and Justin Lin are not to be as court actions continue from Paramount and the Axanar legal teams. The pair had said that Paramount has agreed to drop the lawsuit but apparently that didn't work out as planned. Paramount has told a judge that the lawsuit remains open after the Axanar Productions attempted to get it dropped.
For reasons that still remain unknown Paramount took exception to the plans for a fan funded Star Trek film called Axanar. Usually when there are issues with a fan film, Paramount or CBS will approach the makers and let them know what they have issue with and usually the fans will make adjustments according. I suspect Axanar wouldn't (or couldn't make the requested changes) resulting in the lawyers getting involved. Axanar productions "also filed a counterclaim seeking declaratory relief that its works are non-infringing. However, in an unusual stroke, Axanar also explicitly mentioned Abrams' comments as well as a tweeted statement from Paramount and CBS confirming settlement discussions and indicating work on a set of fan-film guidelines." Declaratory relief asks the judge to decide "the rights of parties without ordering anything be done or awarding damages" which can usually prevent further litigation.
As summarized by trekmovie.com, Axanar Productions is claiming that they need declaratory relief to avoid any additional lawsuits from Paramount and that their screenplay, "Vulcan Scene" and other "alleged infringing works are not 'substantially' similar to Star Trek, or constitute fair use under copyright law. In effect Axanar is asking for the judge to decide in their favor on the case. From Paramount's perspective doing the "right" thing of dropping the suit means losing control of certain aspects of Star Trek. Seeing the lawsuit to its end means they might still lose control of aspects of Star Trek or if they win codify their control for the next generations. Basically, Axanar shot itself in the foot and created a situation where Paramount can't drop the lawsuit.
Now some will see this as a David vs. Goliath thing but in this case I side with Paramount. Like it or not, they own Star Trek and their investment into the franchise over the last 50 years is why we will have six series, 13 movies, hundreds of novels and thousands of tie-in products. Sure they get tons of money back but they could have also put the whole thing into franchise purgatory much like it was for most of the 70s. Also many fan productions have had little problem working with Paramount and CBS on creating their own movies so it can clearly be done. In this case it seems that either money or ego is driving this nonsense and the overall damage to fandom is Paramount will be more likely to prevent fan productions as a way to avoid future risk to their franchise ownership.