When I first heard WB would be doing a Batman series that would introduce lesser known villains into mainstream media including Professor Pyg,a favorite of mine from the "Batman And Robin" comic, I got excited. But when I saw the ridiculous concept art released last year, my enthusiasm dropped. The only reason I decided to watch the show was because, shortly before the pilots release, one of the producers released a statement to the fans, asking, if we liked "Young Justice" and "Green Lantern: The Animated Series," then to give this show a chance. So I decided to that if I didn't like the pilot, I wasn't sticking around. And I am surprised by how good the show really is.
So I went digging through old announcements, and decided to make a list of villains that are set to appear on the show, for the people that have been watching and for those who wish to start when the series returns.
For those who haven't been watching, here's the synopsis (and I'm slightly paraphrasing): Batman must team up with sword-mistress Kitana to face a criminal underworld ruled by Professor Pyg, Mr. Toad, Magpie, Lunkhead, Anarky, The League Of Assassins, Humpty Dumpty, Tobias Whale, Simon Stagg, and Phosphorous Rex.
CONFIRMED VILLAINS:
The Key:

The character will be voiced by JB Blanc. In the comics, The Key is the creator of psycho chemicals that allowed him to access 90% of the brain that is normally unaccessed. In other words, to say he's intelligent is an understatement. He also wields a key shaped blaster and android henchmen.
Man-Bat:
Man-Bat was announced to appear in the series along with the above concept art. In the comics, Man-Bat was a scientist named Kirk Langstrom who invented a serum that transformed him into a humanoid bat. This serum was stolen by the villain known as Talia Head to create an army of Man-Bats for the League Of Assassins (also in the comics, of course). According to Wikipedia, his debut episode will be titled "Metamorphosis." Wikipedia isn't the most trustworthy website, though. Man-Bat will also appear in issue four of the "Beware The Batman" tie-in comic, which will be released January 29. Here's the cover:
King Kraken:
This character was created by Grant Morrison, like many villains on the show. In the comics, this Swedish character, who was once a deep sea diver, was in an accident and now hides his disfigured body in scuba gear.
Gentleman Ghost:
In the comics, Jim Craddock was a criminal from the nineteenth century who was killed by a gunslinger known as Nighthawk. Resurrected as a phantom, he now wreaks havoc on DC's heroes.
Ten Eyed Man:
In the comics, Philip Reardon was a soldier who was blinded in war, until a gifted surgeon was able to hook his optic nerves into his finger tips, allowing him to see once again. He later became enemies with the Dark Knight. Aside from being confirmed to appear in the series, he was also mentioned in a DC Nation short (which wasn't set in the "Beware" universe, by the way).
Axel Alex:
In the comics, Axel Alex was actually an enemy of the Flash, not Batman. He was the second Trickster.
RUMORED VILLAINS:
Solomon Grundy:
Grundy is rumored to appear alongside confirmed villain Gentleman Ghost.
Talia Head:
Talia is rumored to alongside her father, Ra's Al Ghul, who is currently the only A-list villain in the series.
Black Mask:
At one point, Wikipedia claimed Black Mask would appear in the show.
These villains are confirmed to appear in the show (excepted for those under the "Rumored" category above), assuming it isn't cancelled before their appearance. For those haven't been watching, I highly recommend you toon in January, when the series returns with an episode called "Attraction," showcasing the return of the villain known as Magpie. And if the series IS cancelled and the producers have any completed unaired episodes, hopefully they release those on the DVD/Blu-Ray or on the internet.