What is the rationale behind the choice of animation style for The Clone Wars series (2008-2014)?

These excerpts are from this article which describes an interview with George Lucas. To quote a few key excerpts:

One of the big questions a lot of people have about the new series is the look of the animation. Though it's CGI, it's not photorealistic; the characters are made to look like painted wooden puppets (a reference to the marionettes in the 1960s series The Thunderbirds). Lucas addressed this issue head-on:

We didn't want to do photorealistic — photorealistic is what live action movies are. Animation is art. This is an art discussion – either you like photorealistic art, or you like something that tries to find the truth behind the realism. To me animation is about design and style. Our goal wasn't photorealism — we wanted to use computers as paintbrushes.

Lucas also had a lot to say about how the studio put the animation together on a limited budget:

Art is also a technological medium. It has a lot to do with engineering. It's a medium dictated by resources. That was daunting, since we wanted to push the limits beyond anything you've seen on TV. We wanted to take feature animation to television. Normally feature animation costs 20-30 times what TV animation does. So that was a challenge. We had to build a studio from scratch and develop new techniques from scratch. We also didn't make it the normal way you make an animated feature. We treated it like live action feature – editing, rather than storyboarding. It makes a different kind of animated film, since we relied on cutting and editing vs. storyboards. If we can do something that will stand on its own as a feature film, then we've succeeded. He added, rather bluntly:

This series is a test run for the live action series I'm working on. I'm trying to take Star Wars, which was a $50-million-an-hour adventure, and do it for $2 million an hour. It's hard to do that and have them look the same.

This is a different interview, with Dave Filoni (the director) answering some questions:

The style of animation, why did you guys pick this?

Dave Filoni: "Well, it is computer animated but the style of it had to be different. That's the mandate George gave me. He didn't want to do something people had seen before. He wanted it to be unique and stand out. It was a big challenge. But, you know, I worked with really talented people and we collaborated. I'm really happy with the result and so is George."

So from the sounds of it, a mixture of reducing the overall budget for the series, whilst at the same time making it look "big budget", coupled with a desire to do something different is what was behind the animation choices.