First of all: they're ALL great games!! At one point in time I had all three of these games in my gameroom (a varied gameroom with 20 machines total). At one point I needed some space and it was that awful time to sell one of the games. So I have faced the tough decision which one I would sell. Eventually I let the MM go. Here's why:
Twilight Zone is just a great game, but very different form MM/AFM I think. It has a totally different gameplay, much more stop-and-go, it's all based around modes and with a whoppin' 14 modes it's a very nicely varied game. The multiball is not my favourite - the kind where you have to make one hard shot for jackpot, then relight it, then shoot it again, etc. But all in all, the TZ is a legend and a very special game on its own (magnetic flippers, powerball, great wide-body implementation with many shots).
Medieval Madness and Attack from Mars are -in my opinion- very similar games in terms of game design, playfield layout even the rules and flow. The humour is also of the same great quality - these games are FUN! So what are the differences and why did I sell the MM eventually? Well, the biggest difference is the theme: Martians vs Knights. Both very cool and fun themes I think. Also different is the main toy: the castle vs the big saucer. The trolls vs the martians. The huge red dragon in MM. Medieval Madness wins that round for me. It just looks nicer in many ways. As for gameplay, like I said, I find it generally quite similar. The shots are layed out in the same positions with some slight variation. The AFM is the faster game I think. Both games have amazing fun multiballs (where all shots are a jackpot, then finish all of 'em to light super jackpot).
The biggest difference? Price. Reason I let MM go? Uhm. I guess the price. I found both games equally fun and it just came down to the big bucks (euros in my case). Sometimes I regret selling the MM, but I have recently bought a Stern Spiderman and that helps a lot in forgetting the MM.
Good luck with your decision!