AFM and it's not even close. And not that this matters for someone on the hunt for a high-end game but AFM is also the cheapest of the bunch.
They all have fairly similar layouts, great art, themes, dots, sounds.
AFM has the best software by far. It moves you around the playfield requiring you to make all shots - every shot is equally important. It's not incredibly deep yet the replay value is off the charts. The flow is fantastic, and it's an excellent loop pass game. Most importantly it's just fun, fun, fun. Newbies can play it to bash the saucer, better players can avoid the saucer and work Total Annihlation for big points and the hurry up 1 billion, as well as going for multiball and Super Jackpots. Good strategy game with the martian bomb and multiball stacking, and deciding when to go for multiball points or try to take out a saucer, and you always feel like you can get in a groove on 1 ball and turn a crappy game into a good one. Just the right amount of EBs available in factory settings to Rule the Universe as you can expect to lose a ball or two chasing the saucers at the end of a game. Perfectly balanced game in that you can play it the smart way, for points, and on a great game you'll come close to Rule the UNiverse and can decide at that point to go all in and work the saucers.
Idiots and poor players will cry "I get tired of shooting the saucer all the time!!!!" but they don't know how to play it (or lack the skills to play it right) and are complaining about the wrong game, they should be dissing MM.
MB is really cool but it's just too shallow and easy after a while. Fun to play but doesn't have the replayability.
MM has a great toy and people think it's a laugh riot (though I find the "humor" to be a bit overrated and the game overall isn't as fun or funny as MB or AFM), but the software....no matter how many times you play it you'll eventually come to the realization that the only way to play for points is to focus on the castle, and it indeed gets old. In home use you'll surely eventually focus on the wizard mode just to see it but out in the real world if you want to win, it's castle all day, with the occasional multiball you'll use to attack the castle some more. The Trolls are another neat gimmick but they suck, If I actually want to win I usually just time them out.
You don't time anything out on AFM because it's 100 % awesome. It's also got the best theme and sound of the bunch.