It was really only a matter of time, both parties played hardball. Marvel put themselves in the situation because of the contract they gave him for the first one, obviously he wouldn't take a worse contract and Marvel Studios/Disney wanted to keep more. Eventually the studio would have to relent, it was just about squeezing the last penny out of each other.
Am I the only person who thinks that the only Iron Man appearances from now on will be in Avengers films? Marvel Studios has said they will only put out two films a year so with all of the franchises they are trying to start, Guardians of the Galaxy, Ant-Man, Doctor Strange, etc., one is bound to be a hit, maybe not Iron Man big but enough to make a trilogy. That leaves little room for even a reboot of Iron Man, which would be at least five to seven years away at best.