I've never thought Baker was the sole problem. But things have not worked out with him. Even when they had a good lineup, the team still underachieved. Hendry is to blame for constructing the team, but Baker is to blame for making Neifi Perez a regular. Baker and his crew are also to blame for not stressing the importance of quality at-bats. We know hitters develop their plate discipline early in their careers, but we also know Dusty's stance on walks.
To me, Cedeno was probably the most overrated member of the team. He's never had plate discipline, which means a few bad breaks are going to 180 his offensive numbers. He has no business batting second and if there were any better options, he'd have no business being the starting shortstop.