^The Incredible Hulk came out before Iron Man and is thus the first Marvel Cinematic Universe movie.
Re licensing - I kinda recall that the Fantastic Four were in a cartoon without the Human Torch because of he was in a separate show on a different network, so they replaced him with a sort of R2D2 character. Never saw that one though.
Yes, he was replaced with a robot called HERBIE. Spider-Man and His Amazing Friends, made a few years later, also used a new character, Firestar (who was later added to the comic books) instead of the Human Torch. He was supposed to have his own series (Universal were planning a pilot) which was never made.