I have both pins and love both pins, but I would definitely choose ST over AFM. The main reason would have to be the ball interaction between the (2) toys of ST Vengeance against the mothership alien ship of AFM.
You hit the AFM mothership and it shakes, with a knock down bar in front of it and that's pretty much it (pretty cool dmd animation afterwards). However, with the ST vengeance it fires the ball back at you, can freeze the ball and hold it until you hit it again to start a multiball and start a couple of cool modes with Kahn (or Kai, whatever he says at the start of it LOL) modes as well.
Plus, who can forget Klingon multiball and the warp ramp.