Grant was an insanely good general and gets the short end of the stick because Lee was perceived as so great. Lee was a fine general, but often went up against interior generals like McClellan, Burnside, Pope, etc. Longstreet was the best man at Grant's wedding prior and Grant's wife was a cousin to Longstreet: in short Longstreet knew who they would be facing when Grant took command. Lee was fo his own part largely unconcerned and though it mattered little. Longstreet was quoted as saying" that man will fight us every minute of every day for the remainder of the war".
Lee took bold risks no one can deny that but for instance take Chancellorsville. Hooker actually had a very strong plan and it stood every chance of succeeding, It was the merest of chance that it didn't. Missed communications, a division being the weakest on the flank at the time of Jackson's flanking attack. In this case the mediocre O.O Howard and the XI Corp. Imagine if Reynolds with the the I Corp had gotten their in time. This is the first Core, with the likes of "The Iron Brigade" etc who would later save the 1st day at Gettysburg against overwhelming odds. If they were there to brace the XI Stonewall might have ran into a wall. In other words chance is a great determining factor.
Grant had the numbers true, but does a disservice to him in places like Tennessee and at Shiloh in particular. He was a great strategist, a much better one then Lee IMHO. His campaign against Vicksburg is one of the finest military campaigns ever. It was masterfully executed. Of course it could be argued that Lee was just as good and lacked the resources.
In the end it was Grant that won the war with his direction. And when did he win it? At the end of the Battle of the Wilderness in May 1864. Prior to this campaign the Army of the Potomac would turn back northward towards Washington, but he didn't this time. He maneuvered south east to keep the pressure on. This one small change lifted the morale of the entire army. The army finally realized they had the right man and so did Lincoln. No longer would Lee have a chance to fall back and refit. Grant was prepared to keep the pressure on and after the fighting on May 7th he was more or less free to maneuver. And while Grant had Lee fixed in place Sherman was tearing apart the south.
In short in 1864 the best general in the Civil War took the center stage and his name was Grant.