I've really been enjoying the Parker Brothers games for the Atari 5200. So far I have Q*Bert, Gyruss, Mr. Do's Castle, Frogger II, and Star Wars: The Arcade Game.
(I played most of these on the Atari 800 originally, but seeing them for the first time in a long time, and on the Atari 5200, somehow makes them seem fresh.)
I rather saw little, if any, difference between the 5200/computer releases of the games. Maybe a different style title page or game selection or subtle graphic change. But not enough to chase after. Though I did in the day till I realized they were the same! go figure.
It depends on the game. "Star Wars" makes good use of the analog 5200 joystick, so aiming is much more like the arcade. In Q*Bert, you can actually aim the joystick diagonally in the direction you want to jump, which can't easily be done with the CX-40.