>>17848173
A mix of Jefferson Davis playing favorites and the western theater lacking a Robert E. Lee figure. Lee happened to have the ear of Davis, the respect of his subordinates and some skill as a battlefield commander. This all led to him being able to have sway on who was appointed in the east, wheras in the west there was no one to really push back on Davis' nepotism appointments. Albert Sidney Johnston was supposed to be that guy, but he just wasn't suited to command battles of the Civil War's scale which led to him getting himself killed leading troops from the front at Shiloh. It didn't help that Braxton Bragg, a man who feuded with half of the Confederate command and had a complete aversion towards competency, ended up becoming one of the top dogs in the west. I can't recall specific names, but Bragg personally talked Davis out of promoting multiple people who probably would have performed better than the ones they ended up with.
The most frustrating thing though, from a Confederate perspective at least, is that they had multiple competent officers like Joe Johnston and P.G.T. Beauregard sitting around doing nothing during that vital spring/summer of 1863.
Placing John Pemberton in charge of Vicksburg's defense over one of them might have been the single most destructive decision to the Confederate War effort during the entire conflict.