Seems like it wasn't making enough in their opinions. I guess same as Disney Infinity was making money but not the crazy money they thought it should be.
"For more than four years, Marvel: Avengers Alliance has been one of DCPI's most successful games created for Facebook, and our hope was to continue the series with Marvel: Avengers Alliance 2, but the title has not met our performance expectations. As a result we have decided to focus our efforts on new game experiences."
Re: Ugh thread
http://www.gameinformer.com/b/news/archive/2016/09/01/disney-shutting-down-marvel-avengers-alliance-at-the-end-of-september.aspx
"For more than four years, Marvel: Avengers Alliance has been one of DCPI's most successful games created for Facebook, and our hope was to continue the series with Marvel: Avengers Alliance 2, but the title has not met our performance expectations. As a result we have decided to focus our efforts on new game experiences."