The advantage of Antietam is that it was the closest that the Union Army in the East ever came, early in the war, to destroying the Confederate Army in Virginia on a single day.* It really was that close. One sustained breakthrough and Lee's army is hurled against the Potomac and destroyed in detail. And once it's gone, it hardly matters that McClellan would take his sweet time advancing down to Richmond, because Davis really didn't have anything to stop him except, mostly, raw militia and stragglers from Lee's army. It would take several weeks to redeploy forces from Pemberton or (especially) Bragg, Kirby Smith, armies already outnumbered by their opposite numbers in the West, and whatever Davis might cobble together by the end of October would be a small, motley, poorly led substitute for Lee's proud legions, which had the lion's share of the CSA's best commanders.
I'm trying to imagine what a successful Peninsular Campaign looks like. If we take Johnston's wounding as the easiest, cleanest POD, and keep him healthy, the result is a likely a lengthy siege, which is dictated by the strategies of both McClellan and Johnston. The Union would almost certainly win such a siege, but it might take months. Whatever else he was, Joe Johnston was tenacious in defense, and the swampy terrain worked to his advantage through the spring. It creates more uncertainty about the final result and its timing. But either way, McClellan never had the clear shot at decisive victory on the Peninsula that he did at Antietam.
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* You could make a very good argument for First Manassas, but that wasn't given as an option.