Changing the origin of the turtles to being "aliens" is important for several reasons:

• The fact that the turtles are "mutants" is right in the title. They are not Teenage Alien Ninja Turtles. That sounds like another movie to me. One with other characters.
• Changing the turtles from "mutants" to "aliens" changes the entire premise and is a cheap and unimaginative way to take a franchise with loveable characters and remake them in a way that the producers feel fit. It's insulting to the audience that grew up loving the franchise the way it was.
• This is no doubt a production house's (*cough cough Michael Bay cough cough*) way of taking already established and loved characters, jumbling them up with some no doubt contrived ideas, and selling some seats.