Officially, the reason why Disney decided to cut the Marvel: Avengers Alliance and its sequel is because the game was not doing as well as they hope and that they would rather focus their effort on a new game experience instead.
While that sound like a reasonable reason for axing the Marvel: Avengers Alliance games, the fans think that there might be more to it. Some fans seem to think that Disney might be looking to come out with a new Marvel game and since Avengers Alliance is not doing that great, the best option for them is to kill it off so that they can use the name for a brand new game.
Since the Marvel game was not that popular anymore, we could see why Disney would want to end it but their fans were shocked when they announce that they were ending the Disney Infinity game as well.
The game had a huge following and the fans were not too happy with Disney when they made that announcement.