I think they do different things well.
MM and other H!P groups have some pretty decent singer and I care more about individual girls, but we keep getting covers that aren't done well and PVs that could be much, much better; that's usually not the case for AKB (minus the bikini and lingerie stuff, mostly because the covers do show on my iPod but I'd rather have a cover there than not). Music-wise, I like H!P as a whole more, but AKB has very good singles too. H!P is at the top for me, but AKB is also well above other idol groups in my opinion. Well, I also liked Onyanko Club, but it's also Akimoto
Anyway, I don't really need to compare them because I like both and those that think they can only like one and not the other are missing out