I don't think any serious analyst has questioned that Holmgren is pretty dominant in college. The questions have come around whether he'll be able to do the same things against NBA players.
Most traditional big men take 2-3 years in the NBA to get stronger, learn the leverage, etc. We rarely know if they will be really good bigs until then. But Holmgren (in my opinion) is never going to be one of those kinds of centers. So when will we know with him? He gets half, probably more than half, of his rebounds on the basis of his enormous standing reach. That won't go as far against heavyweights who will move him too far out of position. I haven't watched every game, or anything close, but I'm pretty confident that he will be a predominantly weak-side shot blocker in the NBA (unlike, say, Walter Kessler who can stand his ground against other big men). All I've said is that when you start applying the NBA discount to some of his college dominance, he's much less of a unicorn.
I think a lot of us just get tired of people saying that he's the best big man prospect in history. He should go high in the draft. I'm just not convinced that he should be the automatic, unquestioned #1 pick.