Dave Filoni, showrunner of Star Wars: the Clone Wars discussed this in an interview. In short, the Jedi were wildly overpowered and the entire thing had such glaring canonical errors that it was easier to simply remove it from the official canon than try to explain why it was so different to the rest of the accepted stories.
Filoni: The way George explained it to me going in was that THE CLONE WARS micro-series was really an experiment to see what kind of audience there was for Star Wars in an animated form. There have been droids and Ewoks, but that was a long time ago. So he brought out THE CLONE WARS micro-series, and it was super action-packed and exciting and really short installments. And it proved that people wanted to see STAR WARS in a lot of different mediums. So when we into doing this, I think that, now that George is done with the prequels, he wanted to reestablish the rules a little bit more, like "Mace Windu can't take out hundreds of battle droids by himself, otherwise the arena on Geonosis would've been a wipeout; [The jedi] would've won, and there be no Clone Wars. Those are exciting installments, but we don't tie directly into them; we tie more directly into the film that preceded us, ATTACK OF THE CLONES, and the one that comes after us, REVENGE OF THE SITH. We take cues from [Tartakovsky's series]. I definitely pay a big homage to them in some of the design look of it. Anakin wears an outfit that was definitely inspired by what we saw in the other CLONE WARS. But there's no direct link-up.
Mr. Beaks Enlists in THE CLONE WARS with Director Dave Filoni!!
Tartakovsky himself was told that it was to "clean" the canon.
I think George is brilliant. And I think he just wants to ... I don't
know the reasoning, exactly. But from any sense that I can make out of
it, he just wants it to be clean. But there's so much fiction that's
out with "Star Wars," I don't think it would matter."
Tartakovsky Talks About The State Of His SW: Clone Wars Micro-Series