Holyfield would have been a real pain in the butt for Ali. In 12 rounds, I'd go with Ali by a close decision win, something like 115-113, with Holyfield probably rocking Ali good with a left hook somewhere along the line. I'd definitely pay serious bucks to watch that fight, preferably from Ringside. That's two-thirds of my Heavyweight Trinity, Joe Louis being the third.
Ali by UD, but this would be a very tricky fight for him. Holyfield was only a few rungs down from him as an ATG, he had an incredible heart, warrior mentality (that sometimes worked badly against him), a sharp shot, and some really fine moves. Ali would be pretty flummoxed the early rounds by Holy's semi-darting style, and the latter's persistence would bug the hell out of him. By the middle rounds there would be some great exchanges, but Ali's superior hand speed would score more points. Starting in the 9th round things would get ugly, because Holy would unleash the Warrior. I see Ali getting very frustrated, holding, and doing the old neck-pushing, even though I doubt he'd be hit too often there would certainly be left hooks that shook him. 12th round Ali lands a sneaky right that seems to really bother Holy, his knees quake and he doesn't quite recover after. Though he continues the attack he seems to be a bit more hesitant, and he's stopped landing flush. He almost goes down in the 15th and loses that round hard. The decision is UD, but not by a wide margin on any of the cards.