I think the standout issues on that list are trading Billups and JJ in their rookie seasons. Team drafted quality players but didn't wait to try and develop them. Both of those guys had really nice careers, regardless of who was picked after them. Imagine what a team built around Billups, Joe, and Pierce could have done (if they could share the ball enough).
I agree that it's easy to make most any GM look stupid by pointing to guys that were drafted after the team's pick in a given draft. You can only grade these picks based on what was known at the time, though even that is hard because we don't 100% know what was or was not known at the time.
When you see a series of moves or picks that seemed stupid at the time even from the perspective of a fan with limited information, then it gets hard not to hold it against the GM responsible.