The MCU Films:
-Obadiah Stane of Stane International who was a rival of Tony Stark in the comics is turned into his mentor whose been working under Tony's father for a long time. Quite the deviation in comparison to Ra's, who at least took the alias of Henri Ducard - one of Bruce's actual mentors from the comics.
-KGB agent Emil Blonsky was turned into an American army soldier injected with the Super Soldier serum. The Abomination was also a far bigger visual deviation from his look in the comics than any villain in TDKT was. Literally the only thing they have in common visually is the size and the skin color.
-Giving Tony a romantic relationship with Pepper which has never been done before. Pepper's always been Happy Hogan's love interest. Compare this to Rachel Dawes, who at least had Julie Madison aspects incorporated into her and wasn't a problem because Bruce Wayne can literally have any love interest.
-Jarvis (Tony's Alfred in the comics) being turned into a supercomputer.
-Whiplash being nothing like the comics. The defense used is that he was an amalgamation of Whiplash and Crimson Dynamo. I'd like to point out that BB's Ra's al Ghul was an amalgamation of Henri Ducard and Ra's al Ghul but was
still closer to the Ra's of the comics than movie Whiplash was.
-Justin Hammer being literally the exact opposite of the comics.
One is old/cold/serious/British while the other is young/energetic/funny/American. There wasn't a single character in the Nolan films (including TDKR) that was literally the
exact opposite of who that character is in the comics, except maybe Loeb (who is a minor character, especially in comparison to Hammer).
-The Thor mythos being watered down to pseudo-science (Avengers kinda fixed this though).
-Thor's origin being completely changed from start to finish. Instead of the noble warrior with honor who was banished from and intentionally left Asgard because he was sick of thousands of years of pointless fighting and chose to protect the people of Earth, we got a spoiled *****ebag kid that was banished to Earth for restarting a long-ended war.
-While on Earth, he treats everyone like a d!ck and has a superiority complex. Quite far from the warrior that chose to leave his home and put his life on the line for the mortals.
-Donald Blake is nowhere to be seen.
-Jane Foster being a scientist/explorer as opposed to a nurse.
-Loki being watered down and not as mischievous as he was supposed to be (though Avengers did fix this).
-Captain America's sidekick Bucky being turned into Steve's best friend who is also the same age as him. At least in TDKR (which like I said before, I don't count), "Robin" was much younger than Batman and Batman still had somewhat of a mentor impact on him. In fact, the age gap between John Blake and Bruce in TDKR is not that strange since Bruce is 40 in TDKR. In the comics, Dick Grayson/Nightwing is about the same age as Blake when Bruce is around the age of 40 (this is pre-New 52 I'm talking about).
-Red Skull being
ridiculously watered down. In the comics, Red Skull was a menacing fascist bigot on the same level as Hitler and would have even surpassed him in those categories and overthrow him had it not been for Cap. Instead, all of those elements are removed from his character and is turned into a joke in order to have a family friendly film. A lot of you think Scarecrow was watered down but he was
nothing compared to how watered down Red Skull was.
-Overall, the whole first Captain America film having very watered down and/or ignored dark elements of the comics and of the era.
-Black Widow not having the Russian version of the Super Soldier serum in her body (at least there is zero evidence of it so far).
-The BS they pulled with the Mandarin in Iron Man 3. This one is obvious. It is also a lot worse when you consider that not only the Mandarin is Iron Man's archenemy but also that they literally did it to send a political message and for shock value, even if they had to sacrifice storytelling in order to do so.