How to fix this tile job?
There's nothing you can do to fix it short of tearing it out and starting over.  Any sanding or grinding you might try will be even more evident in the difference in finish and texture.

I doubt there is a significant difference in the thickness of the ledger panels.  But even if their is, that's part of the job of a tile setter - compensating for materials and substrate to get an even, clean, finished look.  

I wouldn't be happy with it either.  But it will mean tearing out much of the 
job to fix it.  Good luck.