Spike Brandt, the producer for the show, spoke about this in an interview with AOL TV back in 2011. The interview is cut in pieces so we don't get the full dialog with parts being explained by the journalist who wrote the article. As such it's best to take some of the stuff outside of quotes with a pinch of salt but it does make sense.
In short it appears to be for two main reasons. Number one being because they didn't want to move too far away from the sketch format of old. And number two being because Road Runner and Wile E. Coyote are nonverbal characters so they wouldn't add much to the sitcom setting of the main plot anyway.
If the thought of a sitcom setting is threatening to raise the ire of your inner 'Looney Tune' purist, rest assured that the creators aren't doing away with the skits entirely; each half-hour episode will also feature a CGI Road Runner and Wile E. Coyote short or an all-new Merrie Melodies segment with a beloved 'Looney Tunes' character singing an original song (and in some cases, both).
"We think of Merrie Melodies and the Road Runner cartoons as bonus material, like on a DVD," producer Spike Brandt explained. "They're not related to anything; it's just extra. Because this job wasn't hard enough, we decided, let's make three different shows and smush them all together."
In choosing CGI over traditional animation, Brandt reasoned, "CGI works really well for them because we can create one environment, this desert environment, and basically just shoot different cartoons in it. They're silent characters so we don't have to worry about lip sync. Also, by their nature, they're all about speed and height, so we could do a lot of cool stuff with the camera."
Similarly, because the main plot is very verbal and based on the banter between Bugs, Daffy and their friends, the producers were eager to add another flavor into the mix. "It's kind of cool to have this Road Runner/Coyote section, which is completely nonverbal; it's all based on pantomime, so it's kind of nice," Brandt pointed out.
Since all three segments will stand alone, the producers saw Merrie Melodies as a good excuse to include characters who might not fit into the more traditional sitcom setting of the Bugs and Daffy plot; producer Tony Cervone cited Elmer Fudd as an example, and fans can look forward to seeing him in the first Merrie Melodies short, titled 'Grilled Cheese.'
Cervone and Brandt were emphatic that, despite appearances, 'The Looney Tunes Show' is not an attempt to reset the classic characters that we all know and love -- quite the contrary.
"I don't think we want to reset the tone at all, that's what we want to maintain," Cervone insisted. "But it's important because we did reset the tone a bunch of times [with earlier shows], that's what was always rubbing us the wrong way, 'this isn't who they are -- let's find a format, let's find a container that just shows off who they are.'"