Hello,
I am sorry to hear that you are unhappy with the figure. I have had three different All-Star Superman figures and they all have had the shoulder issue.
The first one I had broke at the right shoulder (take extra caution as the shoulder joints are not ball joints, but seem to be cut joints, as I learned the hard way).
The second one is the one you now have in your possession.
The third one, the one I currently have, is from the box set. I bought this one to replace the other because I liked the shades of red and blue better than the carded release.
As I mentioned though, all three had/have the shoulder issue. I suspect that it's not noticeable in the photo of that one you sent to me simply because it's not a direct straight-on photo of the figure. If you notice, the right foot is a little ahead of the left and at certain angles, the should alignment isn't as noticeable as it is at others.
Here is a photo of the mine and yours that I took right before I listed the figure on eBay. I have just drawn a line across the fists, so you can see where they do and don't line up since it's easier than comparing the shoulders.
As for the emblem being crooked, I can't say as I ever noticed that. The whole figure always just looked off to me, as does the one I currently have. If you would like to return the figure, you of course may do so. Just let me know and I'll provide you with the return instructions.
Again, I am sorry that the figure did not live up to your expectations.