Mario & Luigi: Superstar Saga 3D is a remake of Superstar Saga for the 3DS. It was also made with the intention of celebrating the series 10th anniversary.
As it is a remake of Superstar Saga, the plot is the same. Cackletta wants to control the Beanbean Kingdom and rule the world. Such as such, nothing in the plot is really different, other than Bowletta's sprite remade.
The look of the game is similar to both Dream Team and Paper Jam, but with a little more 3D involved in the look.