IMO, it's just crap writing. They painted themselves into a box on that one, creating an interesting villian and then killing her off because they figured the show would have a short run. Enter the $$$.
Once they got the green light for more episodes, they realized they had messed up and so they just went ahead and destroyed the continuity and integrity of the original animated series.
If it's a question of which comes first, there is no doubt the CW2D version happens AFTER the 3D version running now. Because the last episode is the kidnap of Palpatine from Coruscant which directly precedes ROTS.
After thinking about it, I think Jesse may be right that the 2D version skipped around a bit, timeline-wise.
Someone needs to tell these writers that eventually, somehow, someway, they are going to have to start killing off some of the bad guys, not just all the good guys. IT'S OK TO SHOW THE BAD GUYS LOSE ONCE IN AWHILE TOO!