Richmond
wasn't in the center of the Confederacy, geographically, but it was the Confederacy's logistic center. Nothing compared in the South to the Tredegar Iron Works. Over half the cannon made in the Confederacy were made there.
I've often thought having the two capitals so close, kept the war going more than a year longer. It wasn't just a matter of attacking the enemy capital; it was protecting your own capital too.
Logistically, the Confederacy should have seen their severe shortcomings. They could field an adequate army for the time; they just lacked logistics to fight a then modern war.
As noted, the railroad system through Alabama was terrible, as Jefferson Davis should have easily recognized, when going to his inauguration from Mississippi.
Even more ignored about the Confederate selection of Richmond, was the inability to protect the waterways of the South. The U.S. controlled the steamboats and their production. There was no way, Virginia could protect western Virginia after secession. The U.S. merely had to send steamboats from Cincinnati and Pittsburgh, on the Ohio river, and discharge troops and supplies.
It seemed real folly for the new Virginia defense commander to send a dispatch to Wheeling, Virginia, as if it would be saved for the Confederacy. Wheeling was just downriver on the Ohio river, from Pittsburgh, and just across the river from Ohio.
One should not just question why the Confederates selected Richmond. The question is how they thought they could win independence of not only of the Confederacy, but of Virginia itself. We see volumes on Chancellorsville and Fredricksburg, but nothing about the Ohio river that ran along western Virginia. It is as if no one should ever question what the authorities in Richmond and Virginia were ever thinking at the beginning.