Obviously, the main reason why Disney decided to kill off the Marvel: Avengers Alliance Game and the sequel was because the game was not doing as well as they thought it would. Even though the first game was a huge hit, the sequel was not.
According to Disney, they wanted to kill off the game so that they can focus their time and energy on something that is better. That sounded reasonable enough but some people think that they killed off the game so that they can use the Marvel name to create a better game in the near future.
Of course, Disney has never indicated that they are looking to develop a new Marvel game. Some people believe that Disney wants to stop developing and games and focus on licensing.
Fans were also not too happy when Disney decided to kill off the Disney Infiniti game. Unlike Marvel: Avengers Alliance, the Disney Infiniti still had a huge following when they decided to kill it off.