I have an arcade-in-the-box stick as well as the TE stick.
The TE stick is wider and a little heavier, and opens to reveal the underside of the joystick/buttons that allows easier repairs. It also has a padded bottom that gives it a sturdier base if you rest it on your lap.
The arcade-in-the-box stick is not as wide but it's deeper then the TE stick and the joystick is closer to the buttons. Also, the start/select buttons are on the side of the stick rather then on top. This stick is also available as a hybrid (works on both ps3 and xbox) which is convenient if you play on both systems.
Both sticks are available with the traditional MK bat joystick and convex buttons.