Krause didn't win titles in the 80s either. He also didn't win them after he jettisoned one of the greatest dynasties in sports. I think it was pretty classless, but I also know why it happened. Krause was an asshat. The reputation the bulls got because of him was well deserved.
So the Bulls are probably the only NBA dynasty that didn't die a natural death (aka players get old and they lose in the playoffs and pieces slowly get traded/leave). They went out on top. They won their 6th championship, then the GM jettisons the head coach, and the best player ever retires. The GM can then do what he wants to do and live up his ultimate ego of building a championship team from scratch without inheriting the best player ever.
But what Krause's ego did was pick the worst timing ever to go and try and do it. Of course this is all hindsight because you don't truly know what you're getting, but the 1999-2002 drafts are some of the worst drafts in a row in NBA history in terms of what they produced. Of course Krause also thought 2000 free agency would save him if the draft didn't.
The Bulls had the #1 pick in 1999, and took Elton Brand. He was a solid 20/10 guy for awhile, made an All-Star team (as a member of the Clippers), but that was basically his career. He wasn't leading any team anywhere. The Clippers topped out as a second round team with him. The other best players of this draft are Shawn Marion, Manu Ginobili, Andrei Kirlenko, Jason Terry, Andre Miller, Baron Davis, Lamar Odom, and another player the Bulls took in Ron Artest (now known as Metta World Peace). Ron Artest was a very good pick at 16, but of course had all the mental problems. This draft produced no superstars.
The 2000 draft is one of the worst drafts ever and the Bulls took Marcus Fizer who fizzled out of the NBA after his rookie contract. The Bulls also acquired Jamal Crawford in this draft as they had another pick as a result of trading away Toni Kukoc. Crawford had a long solid career, but never made an All-Star team. The best player in this draft is Michael Redd, who was drafted 43rd overall. A few other solid players taken in this draft are Mike Miller, Hedo Turkoglu, and Kenyon Martin, but they were primarily role players in their careers.
The 2001 draft did produce one 2nd tier star who the Bulls had an opportunity to take, but didn't. That was Pau Gasol at #3. The Bulls instead traded their 1999 #1 pick (Elton Brand) for the #2 pick in Tyson Chandler... who would later become an All-Star and Defensive Player of the Year a decade later, but not with the Bulls. The Bulls actual pick in this draft, #4, was used to take Eddy Curry, who was out of shape, couldn't rebound due to his inability to jump, and just never lived up to his nickname when he was drafted (Baby Shaq). Other than Joe Johnson taken at #10, this draft is mostly known for its later picks in which Tony Parker (#28) and Gilbert Areanas (#31) were multi-year All-Stars.
In 2002, Krause's last draft, the prize of this draft was Yao Ming. The consolation prize was considered Jay Williams. The Bulls won the #2 pick in the lottery and thus took Williams. He had an okay rookie season, but then rode a motorcycle and ended his career after crashing it. Yao Ming was forever injured in his career and the best player out of this draft was again a 2nd round pick at #35 named Carlos Boozer (who would later play 4 years for the Bulls). Amare Stoudemire was a close second, and probably had better overall seasons than Boozer ever did. Outside of that this draft is also fairly garbage in terms of star power.
Krause resigned after the end of the 2003 season. His team had improved enough to win 30 games and basically shot itself out of lottery contention in an absolutely loaded draft. They finished as the 7th worst team and ended up with the 7th pick, with the Top 5 picks being highly coveted.
The Bulls basically tanked for three seasons, won the lottery balls once, and got fucked over in the other two by getting the lowest possible pick (#4), but it didn't matter because these drafts all sucked anyways. Add in that utterly failure of the 2000 free agent summer, and you get this utter flop by Krause's ego. At least he had the decency to resign because Jerry Reinsdorf was never going to fire him.
Things may have gone much differently had Krause gotten his way and traded Pippen years earlier. But, there's also the matter of does Michael Jordan come back if Pippen is traded in 94, or after the 97 season.