The issue is, while Star Trek has always been good at wonderful special effects sequences, the series and movies have always been more about the its commentary on humanity and our society. In Star Trek's futuristic world, we have outgrown the petty squabbles of our present day, and have moved on to become an evolved and resilient race.
The 2009 movie satisfies with great character development, and because of the story it pursues, it doesn't necessarily need to go out of its way to emphasize the franchise's idealistic vision of humanity. However, I would not like to see that integral part of that original vision diminish in favor of more action, adventure and special effects.
On the other hand, the Star Wars movies have always fit the standard blockbuster framework, so I'm sure that J.J. will do a great job with it. If nothing else, he will definitely put episodes I-III to shame. Of that, I am confident. But with both movie series under his direction, will the vision for the two series converge, making Star Wars and Star Trek feel too similar?
After all, 2009's Star Trek already began to lean towards that Star Wars formula. It was a lot of shoot-'em-up, and it had less complicated, more evil, villains. The pacing was faster than I'm used to from Star Trek, and it lacked much introspection.
I don't want Star Trek and Star Wars to be similar. I admit, I feel a certain superiority when arguing Trek's advanced plot points and messages. Were Star Wars to be that good, assuming J.J. could raise the quality of the new Star Wars to the middle ground that the 2009 Star Trek occupied, balanced between what the masses want and wonderful writing, it removes the advantage Trek has, and gives those smug Wars fans new fodder. If the opposite happens, and Star Trek is dumbed down to the level of Star Wars moving forward, continuing to push it away from its roots, the same thing will happen.
I am concerned that J.J. will, intentionally or not, keep nudging Star Trek from its original vision. Who's to say it won't go further once his time becomes divided between the two, with the worlds merging in his head?
They are both sci-fi adventures full of aliens. Even though one supposedly happened a long time ago in a galaxy far away, to paraphrase, it looks futuristic enough to be confused with our not-too-distant future to the untrained eye. It wouldn't be that hard to make a lot of the same choices when developing the projects, and end up with two very similar film series. I don't think he'll use the same actors or sets, but with the gleaming white new Enterprise reminding me of Star Wars spaceships, there could be a similar color scheme and visual component.