I'm going to sound a bit hypocritical here, but even though I'm a bit of a stats nut, we can't always judge purely on stats, because there's a fair few variables that effect them. Teammates and style of play being main ones (just look at those that think the D'Antoni system skews things), apart from actual ability obviously. You can judge by actually watching Bogut play too, and he doesn't look 'lost' or like he's getting 'left behind' to me, like guys like Olowokandi did or Kwame Brown can still do. And I think he has more of an impact than someone like Bargnani does on the court, stats wise or otherwise.
I actually think Joe Smith is underrated, simply because he's maintained a solid level of play throughtout his career, without much dropoff really now that he's getting older. There are much bigger draft busts than him. In 1995, people thought that the Timberwolves were nuts taking a high schooler like Kevin Garnett at #5 in the draft. It obviously worked out well, but nobody thought he'd become the player he was/is, even in his first season. Joe Smith never had massive potential beyond what he already was to begin with, so it's not like he's never lived up to what people expected. He just isn't the superstar that many #1 draft picks are. And much like the Bucks in 2005, I think the Warriors probably made the right pick in 1995. Apart from Antonio McDyess or possibly Rasheed Wallace, I don't really think any of the other top picks would have been the right choice to make. They didn't need guards like Jerry Stackhouse or Damon Stoudamire, as they already had stars such as Latrell Sprewell and Tim Hardaway (although both would have left Oakland within a couple of years). As I've said, Garnett was somewhat of a questionable comodity at NBA level, and Bryant Reeves wasn't quite #1 material, especially considering they already had a decent centre in Rony Seikaly. And I think college stars like Ed O'Bannon and Corliss Williamson (although he carved out a pretty decent career) wouldn't have really been the right choice either.
As for Yao, I think he would be (and probably still is) much more harshly judged, mainly because he is 5 inches taller and 50 pounds heavier, so people assumed he'd dominate on physical size alone. The truth is, he's much more of a finesse centre than people expected, and he's not just going to overpower people with brute strength like Shaq, because he's simply doesn't have that kind of power, despite his size. Still, Yao is clearly one of the most effective inside scorers in the game, and his main weaknesses IMO are endurance (which is to be expected with a guy his size) and durability (again, probably to be expected with a guy his size). I think expectations for Yao have always been unrealistic, but the reality is he's still among the very best centres in the world right now.