How long did you play the 3DS for? You have to give your eyes some time to get used to this new way of viewing. And even then, not everyone will have the same experience, so even if you have trouble with the 3D, that doesn't mean everyone will. I don't. 3D affects everyone differently. Everyone's eyes are different.Speaking strictly about the 3D effect, I found that it was very difficult to focus on. Your Mii/plane is very close to the screen while there is a fair amount of depth in the background. Unless you unnaturally relax your eyes, it's very hard to focus on both at the same time. 3D can only be effective if the user can forget about it, i.e., you shouldn't have to think about it.
Gameplay-wise, I wasn't thrilled either. Even though I like slow-paced games, the fact that there's a time-limit for each of the missions (and even in Free Flight Mode!!) totally ruins it. Why would you call it "free flight" and time it at 2 minutes? I know you can extend it if you run into white clouds, but I think it's still a pretty stupid idea.
And the time limit is only present in the demo, because, well...it's a demo. I don't believe it's in the retail game.
And can we not turn my thread into a ten page argument? Just putting that out there in advance, just in case.