Quoted from RobT:
There is no doubt that AFM has better balanced scoring.
But in a home environment, who cares? I always play MM and AFM for the wizard modes (Battle for the Kingdom and Rule the Universe) more than I do score. Of course to get to BFTK, it means you have to defeat all the castles anyway.
Actually, even when you take out scoring I like AFM better. When you take scoring out and go straight for the wizard mode, I feel like the game devolves into this "start multiball, hit the castle as much as possible" sequence that you just rinse and repeat over and over. In fact, regardless of whether you're going for scoring or the wizard mode, pounding the castle is one of the best strategies. Because of that, it's not one of my favorite games...I feel like every game kind of plays out the same way. I could play it differently, but why? Wizard mode and points both favor the multiball castle attack.
AFM though on the other hand has some things that make it more difficult to do the multiball strategy like that. One, you have to collect a super jackpot to make it to the wizard. That by itself means that you can't just ignore jackpots in multiball. Second, the ships don't respawn during multiball, you can only kill one per multiball, whereas in MM you can kill all of them if you're good enough. AFM also requires a 5 way combo, so getting that going also requires some thought. Basically, the goals are more varied so my games aren't all the same. Now I've heard that destroying the last couple saucers can get monotonous but I've never made it that far or played enough to find out (although I have made it BFTK in MM).
I'm definitely in the minority in my feelings though, most people prefer MM. And in a tourney I would rather play MM, a lot of people are unaware that just shooting the castle is better than actually hitting the jackpot shots for the most part unless certain things are setup.