I've had my AFMr for over two years and it's not going anywhere. I just sold my MBr and I had it for just under a year.

My main issue with MB was the main multiball mode (Frankenstein Multiball). It's actually a grind when you start it and its really easy to start. Too easy. Getting super jackpots is as easy as hitting Frank and you have to hit it a number of times to collect his instrument. I would try to avoid hitting the Frank standups until I had a least one other monster mode going. At least then I would have something to shoot at that was interesting and worked towards achieving a goal.

With AFMs main multiball, there are at least interesting shots to make. Make all the main shots, then hit the roaming shot for super jackpot. Plus you can also have the motherships shields down and collect shots against it, blow it up, and maybe trap and extra ball behind the shield before it goes up for a chance at dirty pool. Way more fun to play than MB multiball.

For the rest of it lets compare features:
AFM
bouncy Martians/martian multiball - Always fun, love it!
Strobe Multiball - One of the coolest modes in pinball, if you're in a dark room.
Video mode - Meh. At least it doesn't come up too often.
Total Annihilation - Fun, love the callouts and sounds.
Mode Hurry-ups - Cool
Blowing up motherships - Cool, but a little repetitive
Attack Mars - Always exciting for me, since I rarely get to it. Its a nice change-up from just blowing up the mothership. I like the visual with chunks of mars blowing off with each ball hit.
Rule the Universe - Basically TA, but with Rule the Universe dangling in front of you. That makes it really exciting.

MB
Collect monsters - Cool. I like the variation in the lights, songs, and shots for each. This is why I kept the game for a year.
Collect their instruments - Nice challenge, though in most cases, it was just hitting the same shots that collected the monster.
Mosh Pit Multiball - This is the best mode on the game IMO. Progressive balls and you actually get to use the Frank ramp to collect.
Monster Bash - Yah it has a cool intro, but the song grinds on my nerves. I want some real thrashing metal here.
Monsters of Rock - Same as above
lyman's lament - Meh

Too me there's really no contest, AFM all the way. Though MB wins on looks by a landslide. The best looking game I've ever owned.