Sounds like your player is just min-maxing there character. It can be done with just about any character and has been around since there very beginning of Pathfinder.
So to your question, "Is Pathfinder becoming unbalanced?" the answer is no but yes. It has always been this way. Granted to get to what your player is doing it does take some time and effort.
Now some others have already stated that which creatures you through at them or how the battle field is set up can change a encounter to a major degree. From your description it sounds like this character is taking care of the enemies before the other players have a chance to do anything, correct me if I am wrong. You could write up an encounter where the enemies are something that Mr. McBeatstick has trouble with that others can deal with easier.
Also I just re-read what you posted and realized that your main point was about the CR system and if it is unbalanced and needs to be reworked. I would have to say yes and no. Yes, because with everything that has come out and that it has been eight years since the system had been implemented it does need some tweaking. But I also say no because it was also, in my mind, a guide line to help with the building encounters and to help new DMs learn to create there own encounters.