Well what you are looking at are raw stats which do not take into account he plays half his games in the worst offensive park in baseball. Apparently you do not take that into account either. Something you still should have noticed though is his OBP is much higher than anyone but Wright. This is a huge advantage for him over Freese, especially when park is considered. OPS+ shows him to be better than Freese to date and he is a better defender than Freese.
Here is an example for you. Home his slash is 266/366/370, but the NL as a whole is only 227/303/341. While you may consider his home numbers poor, this shows they are well above average for Petco. He is an outstanding hitter for the park.