A good deal, I'd say. It's worth noting that McClellan beat Lee in western Virginia very early in the war, which set up the creation of West Virginia and its incorporation into the Union. McClellan was certainly too hesitant on the Peninsular Campaign, believing his army had been unnecessarily weakened to protect Washington D.C. from being attacked by Stonewall Jackson through the Shenandoah Valley. The Army of the Potomac still held a distinct numerical advantage, however.
"Prince" John Magruder, a theater actor, used some of his own theatrics to convince McClellan he had significantly more men than he really had at Yorktown, delaying the Union Army for a month. In any case, Lee didn't come into the picture until he assumed command when Joseph E. Johnston was wounded at Seven Pines as the Union Army neared the outskirts of Richmond.
Lee was derided as "Granny Lee" and "The King of Spades" by his men for digging in around Richmond. He ordered J.E.B. Stuart, however, to encircle the entire Union Army and perform reconnaissance, which led Lee know McClellan had positioned his forces on two sides of the Chickahominy River, wasting his numerical advantage. Jackson returned, exhausted like his men, after one of the most remarkable campaigns in American military history (The Shenandoah Campaign), outmaneuvering several forces sent to block his advance and essentially wasting their time. In any case, Lee used his superior intel to push McClellan back in the "Seven Days' Battles" despite the fact that McClellan had the numbers (he believed himself outnumbered several factors to one, the man appeared a bit off his rocker with his gigantic grudge against Lincoln).
A Western general, John Pope, was brought in to take over, but several of his subordinates arrived piecemeal to what became Second Bull Run, and McClellan is suspected of sabotaging Pope's Army so he would be reinstated as commander of the Army of the Potomac. He has also had Winfield Scott, maybe the best mind in American military history, oustered as general-in-chief out of sheer selfishness, despite his "Anaconda Plan" eventually being how the Confederacy was defeated.
The big screwup for McClellan is at Antietam. He was able to obtain Lee's plans when some Confederate officer apparently left them rolled up in a package of cigars, and said something to the tune of "I'll surely whip Bobby Lee now." The battle plan at Antietam was all screwed up, however, sending Hooker on a huge initial attack in the Corn Field, then a center attack, then Burnside to beat his head against "Burnside's Bridge." This allowed Lee to use interior lines of communication to shift his defenses to deflect each attack successively. A potentially fatal opening developed in the Confederate center, but McClellan's friend, Fitz John Porter, said "Remember General, I command the last Army of the Republic," and McClellan declined. Burnside finally forded the creek and was ready to roll up Lee's right flank, finally. Just then, AP Hill's oversize division arrived from Harper's Ferry and hit Burnside on the flank. This allowed Lee to make it back to Virginia with his army intact, escaping the Union's best chance at wiping him out with knowledge of his plans and a large numerical advantage.
Burnside told Lincoln he was unfit to take over command, as McClellan was now out. Lincoln thought this kind of humility was just what the army needed after "little Mac"'s arrogance. Burnside was right, though, he spent too much time crossing the Rappahanock and let Lee take a decisive defensive position and just threw his men into a meat grinder. After him, Hooker did a much better job seizing the initiative and restoring confidence to the Army, but completely lost his nerve at Chancellorsville when a cannon shell struck his headquarters.
McClellan was a good organizer and instructor, his men loved him, but he was terrible at gaining intel on the enemy, had somewhat sympathetic leanings toward the Confederacy as a Democrat, and was horrible at gaining the initiative, moving quickly, surprising the enemy, all hallmarks of good commanders (which Jackson showed). Yes, his army was large and unwieldy, and logistics make rapid advances difficult, but being overly cautious is a good way to ensure the war would drag on, indecisively, as it did. Burnside was just an unimaginative putz, quite frankly, and unfit for the job. Lee and Jackson's gamblers' spirits and innovative offensive maneuvers were the perfect counter and necessary to overcome their numerical disadvantages.
Obviously, there's a ton of reading on this, but Battle Cry of Freedom by James McPherson is a great one-volume history. Stephen Sears: Landscape turned Red: The Battle of Antietam is another one.
Later in the war, McClellan and Clement Vallandigham posed a huge threat to the Union cause as it bogged down in the Atlanta and Overland campaigns. Although McClellan insisted he would continue to prosecute the war until the CSA gave up its claim to sovereignty, it seems he would have allowed it back into the Union with slavery. For many, especially as attitudes about slavery were changing through 1864, this would have meant the Union "lost" the war.