Avatar still has the same problems that all 3D movies do, panning problem, blurriness, focus problems, and eye strain/headaches for many people. Avatar's 3D was better than all 3D before it but it still sucked.
I didn't notice any of the things you complain about with Avatar. I thought it looked spectacular.
It's hit or miss, depending on the person.
Panning is a problem for the reason for the reason of technical limitations. It'll be that way until holographic 3D imaging is reality, if that's even possible. Directors will use various tricks to try and minimize it, but I don't see the problem being possible to be fixed 100%.
Focus problems? Bullshit.
You can't have everything in focus, not if there is anything in the foreground. So, with movies, if stuff in the foreground is in focus, the distant background can't be in focus.
If there is stuff in the, well, middle ground, and beyond, that all can be in focus. It's an optics issue.
When that gets put into 3D, the perception of depth is exaggerated thanks to this very real issue of optical focus. The director focuses on what needs to be clear, what is and is not in focus is at the director's discretion, and that of the director of photography.
And this helps bring the foreground out of the screen, and create a sense of distance and depth to anything behind what is in focus.
Headaches and such? I'd argue anyone getting headaches was NOT following what the director wanted, i.e. focusing the eyes on what is in focus. My eyes were going all over the place, looking around and enjoying the perception of depth, but still managed to basically keep vision locked on the focused subject, and I had no headaches.
There was also an article suggesting that very fact, which I had read prior to seeing the movie. So I knew to focus on the subject that was in focus on the screen, and that proved to work.
Some people are going to get eye strain, but that's not a problem of bad 3D, that's a problem of 3D on a flat display, period. Some people can't grasp how to manage the eyes.
Again, you can't solve that, except with projection of 3D into a 3D space, not onto a 2D surface.