BTW on the Tartakovsky thing, it was made to fit to the events of ROTS... I don't see how the 2D cartoon doesn't fit within the storyline, so for my money it's something I enjoyed so I still consider it a major part of Star Wars. I don't think the show conflicting with the release of the 3D one had any issue though.
I thought the Tartakovsky cartoon ended simply because it was done. They closed with the "end" of the Clone Wars, more or less right into ROTS. I could be wrong as I don't recall when it even came out though. I thought 3D came out a good while after 2D was out. There's 3 years for the Clone Wars to take place though, and plenty of time for those short toons to squeeze into that timeline easily, to me.
Based only on what we ended up with from the 6 seasons of The Clone Wars, I think in terms of in-universe timelines and such it could be made to work with the micro series. The only big issues that stand out to me at the moment are Grievous' cough, which he has throughout the TCW series yet it is caused in the final episode of the micro series, and possibly the two Battles of Mon Calamari. We really needed to see what TCW would have done for the Battle of Coruscant/pre-ROTS to know for sure if it would have contradicted the micro series.
Neither cartoon series really jived with the other EU (comics and novels), so in that regard it might be nice if The Clone Wars is the only super-duper official canon for that time period. No worrying about Alpha, Durge, Ventress' origins, Labyrinth of Evil/micro series Battle of Coruscant, Mandalorians, 2 Kamino or Mon Calamari battles, or Barriss Offee issues.