It's a good question. I think that Naruto is pretty dumb (Please don't hate me Naruto fans!! :P) and don't really understand its popularity. Maybe it's because it appeals to a wider age group. Or because it's still going on, unlike FMA which is over now (unless you count the manga). I haven't actually seen Inuyasha (and have no desire to) so I can't really say anything about that. But you're right... Fullmetal Alchemist is a quality anime and probably deserves higher recognition.

I used to like Inuyasha but quickly lost interest in it. I like how short FMA is (in comparison to other animes, like Bleach or Inuyasha). The story and characters in FMA is so interesting... And it's not as confusing as something like Inuyasha, and sticks with basically two main characters (Ed and Al). I mean, you could argue with Mustang and stuff, but really it's all about Ed and Al. I kind of like that about it.