He was. I tend to think Lee was the greatest commander of the war because he did so much with so little. However, one reason Lee had that one great year of victories was that all the Union commanders before Grant (and Meade) would retreat even though they outnumbered the Confederates in men and materiel.
No Grant was far better commander then Lee.
Lee was prmorted past his competency level. He would of been much better staying as an Army Geeneral and someone like Albert Sidney or Joe Johnson being the over all commander.
Lee never grasped the war was national in scale. He focused on Virginia only and, arguably, cost the South the war by refusing to look at the strategic picture.
In addition, Grant understood the strategic priorities of the North in a way Lee never did for the South. Lee’s biggest failing, like the French in WW1, believed offensive warfare was the key. He never understood that given the South deficits in material and manpower, he need to win by outlasting the north. Fredricksburg, and possible 2nd Manassas were Lee’s only true victory. In the rest of his battler he continually lost a greater portion of his force then the North. The result is all of his victories were Phyrric. They won a short term respite in exchange for irreplaceable casualties.