Naruto. Full Metal Alchemist is good, but I prefer Naruto.
The main reason for this is the characters. There are so many characters in 火影忍者 (including Shippuden) that are so awesome. I like Ed and Al, but... they're just not the same.
There are other reasons, though. The depth of Naruto's plot is breathtaking and it is full of great twists. It's quite unpredictable. The duration of 火影忍者 and 火影忍者 Shippuden together allow for a deeper plot than Full Metal Alchemist, of course, but even if Full Metal Alchemist continued for as long as Naruto, I think I'd still prefer Naruto. Again, this is mainly due to the characters. From the lazy genius 鹿丸 to the funny and positive Rock Lee... There are very very VERY few 火影忍者 goodies I don't like, compared to the ones I do like.
I 爱情 the art style of Naruto, as well. In Full Metal Alchemist, sometimes many of the faces all look the same. There's just something really nice about the faces in Naruto.
火影忍者 can be hilarious, too. This is seen 更多 in the original 火影忍者 series than in Shippuden, but it's still there. Full Metal Alchemist can be funny, too, but the humour in 火影忍者 just seems to appeal to me more.
I can't think of a single reason not to like 火影忍者 (other than the fact that Sasuke and Sakura annoy me). It's just... wonderful.
Both 火影忍者 and Full Metal Alchemist are some of my favourite anime, though!! They deserve their popularity. :)