The DCAU Flash has been severed from the "Flash legacy" that exists in the books, making our Wally the only speedster around. The Reverse-Flash is the villain that most represents that legacy, so it's no wonder they didn't bring him in. Think about it: they've got a Wally West that exists with no Barry Allen coming before him. Eobard Thawne wouldn't be effective as Wally's enemy, and Hunter Zolomon wouldn't exist without Thawne before him.
Of course, they could've just done something very, very different with the character. Ultimately, they just never got to it.
"Excuse me, I'm sorry, I thought I just heard a line I wrote."
George S. Kaufman