E.P. Alexander should definitely get the the signal command trait. He was the guy who designed and operated Beauregard's signal corps at Manassas. Unlike the Union signal corps, Alexander's corps was operational before and during the battle. He was the protege of the man who would go on to develop the Union's signaling corps. Once the war started Alexander took all his knowledge with him South and set up the first signaling corps for the Confederacy. He didn't remain the leader of the corps and in fact another system was devised by another guy, but Alexander was one of the really technology, science brilliant Confederate generals.
Entrencher might be another ability he should have. He helped to build the works around Richmond and was constantly building temporary earthworks throughout the war (Longsteet's and Lee's artillery leader).
I rate him a 4-2-4. Maybe a conservative rating would be 3-1-3, rather than his in game 3-1-2.