Some changes sure. Not as many as you list though.
BTAS did it. Their villains were given new personalities, origins, and some were "drastically changed" from their comic book versions. No one seemed to mind that Mr Freeze, Clayface, Catwoman, or Clock King were drastically altered. Not to mention Poison Ivy, Two-Face, Killer Croc, the Riddler, Mad Hatter, Hugo Strange, Count Vertigo, and many more were altered for the series. It is not unusual for a series to change the characters around a bit when adapting them, since they're different mediums and what works in one doesn't necessarily work in the other.
So I don't see why that's a problem because every other comic book series under the sun has done it, and it’s worked out pretty well for them.
While you may not consider it a problem, I do. And I think that's the fundamental difference.
BUT, let's look at the list you presented:
1) Mr. Freeze -
Freeze is a scientist who must wear a cryo-suit in order to survive, and bases his crimes around a "cold" or "ice" theme, complete with a "freeze gun" that freezes its targets solid. In the most common variation of his origin, he is a former cryogenics expert who suffered an accident while attempting to cure his wife. His original origin and characterization was that Mr. Freeze was a scientist who inadvertently spills cryogenic chemicals on himself, resulting in his needing
subzero temperatures to survive. The ONLY thing BTAS did was give him a wife. Basically, since they were no longer hindered by the old CCA rule that villains couldn't be relatable or sympathetic, they could give him some depth. Not really much of an alteration here.
2) Clayface - I'll give you that one. Even though the character was basically Basil Karlo and Matt Hagen merged into one character given a new, again TRAGIC, backstory.
3) Catwoman - Can't give you that one. Because in the show she's given NO story whatsoever. All we know is she's a cat-burglar with a soft spot for animals. And considering she's had around half a dozen origins retold over the years, I'm glad they didn't give her one in the show.
4) Clock King - totally right! Can't make a single argument against it. And you know what, this version of the character was boring, completely uninteresting and just simply lame.
5) Poison Ivy - In the comics she was a promising
botanistwho is seduced by Marc LeGrande into assisting him with a theft. Fearing she would implicate him in the theft, he attempts to poison her with the herbs, which are deadly and untraceable. She survives this murder attempt and discovers she has acquired an immunity to all natural toxins and diseases. Her origin was rewritten in1988, where she was given the name Pamela Lillian Isley. In this version she's still a botanist who gets double-crossed by a man and develops an immunity to all natural toxins and diseases. She specializes in hybrids and can create the most potently powerful floral toxins in the world. Often these toxins are administered in her preferred way, a poisonous kiss, usually after professing false love or affection for her victim. They come in a number of varieties, from mind-controlling drugs to instantly fatal toxins. So, I'm gonna go with this one not being much of an alteration.
6) Two-Face - Is still a handsome DA who is horribly disfigured because of his attempts to thwart a Gotham Crime Boss. Switch Falcone with Rupert Thorne and you're good to go. Sure, the acid was changed to an explosion. But the story is more or less the same. Also, in the 1980s, Harvey's origin, presented in
Batman Annual (vol. 1) #14, served to emphasize Dent's status as a tragic villain, with a back story that included early struggles with bipolar disorder as well as paranoia. So, I'm gonna say the show is pretty close to the comics.
7) Count Vertigo - He's Vertigo in this show. And he's still a gimmick-villain, like he always was. And Vertigo method of attack is to cause the distortion of visual perception and the loss of sense of balance. The "Vertigo Effect". The only major change in the show is that he is involved with the Society of Shadows. So, not so much of a change there.
8) Killer Croc - Yep. I'll give you that one too. Can't argue at all. And you know what... I hated this version of Killer Croc. He was a moron generally only there for comic relief. Though the episode where he tries to get revenge on Bullock was mildly enjoyable, although completely implausible.
9) Hugo Strange - His original iteration was a mad scientist who did all sorts of dastardly evil mad-scientist style experiments to commit horrible crimes in Gotham. Thus the name "Strange", thus another generic gimmick villain. His post-crisis incarnation was introduced in the "Prey" story-arc as a psychiatrist who, while brilliant at his work, was portrayed as being equally psychotic. Strange becomes obsessed over Batman. Conducts evil schemes involving brainwashing people, and deducing Batman's true identity as Bruce Wayne. In the end though, Batman managed to foil Strange's plot and forced him to doubt his own conclusion about his true identity, before he could share it with anyone else. Hugo Strange is introduced in the episode "The Strange Secret of Bruce Wayne", a remake of the auction that took place in the "Strange Apparitions" story arc of the 1970s. So, good enough for me.
10)Mad Hatter - Jarvis Tetch is a man obsessed with the book
Alice's Adventures in Wonderland and its sequel
Through the Looking Glass, particularly favoring the chapter 'A Mad Tea Party'. Tetch often quotes and makes reference to Carroll's
Wonderland novels, and sometimes even fails to discern between these stories and reality. He has a pet named Carrol Lewis. And throughout his early appearances and reappearance in the 80s, he shows a penchant for kidnapping and brainwashing, including doing both to Lucius Fox. In the story, "All My Enemies Against Me" in 1981, his mind-controlling hats are introduced. Tetch is shown to kidnap Barbara Gordon and forces her to play the role of Alice in his recreation of Wonderland (though that was 1996). AND he didn't really have an origin in the comics until around 2004 and onward. So, there's not much to contradict. So, I'm going with a big nope on Mad Hatter.
11) The Riddler - The ONLY difference between Riddler in BTAS and the older comics is his attitude. Because in the comics he's often shown as a cackling madman. This change was made specifically to separate him from Joker and from the Frank Gorshin '66 portrayal (as evidenced by info found in
Comics Scene #43, published by Starlog). Throughout his Golden and Silver Age portrayals, The Riddler is typically portrayed as a smooth-talking yet quirky character, motivated by a neurotic compulsion to commit crimes based on riddles and puzzles. The Riddler is obsessed with riddles and word games. He delights in forewarning both Batman and the police of his capers by sending them complex clues. The character is depicted as wearing a domino mask with a green suit and bowler hat, or a green unitard with question mark prints. He doesn't get much of any sort of backstory until "The Long Halloween" and afterward. So, again, I'm gonna go with Nope. Not much in the way of changes.
So, all in all, 3 of the 11 characters you listed were definitely drastically altered. But that's really it.
And the 3 listed, I felt were worse for it.