Well like I said, 2000-2012 was ROUGH. But I think the point of your post is to indict the current regime but those years aren't their fault. Also, I think people's viewpoints on this get warped because there really just isn't as much homegrown talent out there as people think. Teams make a ton of trades, FA signings, dumpster diving, etc. to build their rosters.
I didn't want to get into this too much but let's look at a couple other teams.
Yankees
Judge was picked in 2013. But who else? Geezers like Gardner who was a 3rd round pick in 2008 and Cano who signed in 2001? Ok, we are using your arbitrary "turn of the century" language so they count. Who else? Gary Sanchez? Luis Severino? They suck.
Rays
Everyone's draft and development darlings. Evan Longoria, Carl Crawford, Kevin Kiermaier, David Price and Chris Archer are probably their top 5. That's pretty darn good but it's not THAT much better than ours and you think we are one of the worst.
Cubs
Let's do a good but not great franchise over the past 23 years. They did have some good bats. Kris Bryant they got with the #2 pick in 2013. Javier Baez with the #9 pick in 2011. Wilson Contreras in 2009. I'm not even sure who their best pitcher is. Maybe Mark Prior who was drafted in 2001 and had a few good years before his arm exploded. Jeff Smardsija had about 7 WAR from 2006. So you probably have to use more bats to fill out the Top 5. Probably Ian Happ in 2015 or Geavonay Soto in 2001? Seem pretty comparable to us.
Angels
Let's do a bad team. The Angels are supposedly the worst at developing talent. And they are but not if you go back to 2000. Jered Weaver in 2001, Howie Kendrick around then, Mike Trout in 2009, a few others that are decent and basically nothing since Trout.
A's
They are bad at this game but make it worse because their best guys they traded for nothing. Donaldson and Chapman to us and Olson to the Braves. Best pitchers are probably Sonny Gray and Joe Blanton.
It's hard to know who was drafted and developed at a glance so I could be missing someone from the above teams but you get the idea.