Naruto. Full Metal Alchemist is good, but I prefer Naruto.
The main reason for this is the characters. There are so many characters in Naruto (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 Naruto and Naruto 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 Shikamaru to the funny and positive Rock Lee... There are very very VERY few Naruto goodies I don't like, compared to the ones I do like.
I love 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.
Naruto can be hilarious, too. This is seen مزید in the original Naruto series than in Shippuden, but it's still there. Full Metal Alchemist can be funny, too, but the humour in Naruto just seems to appeal to me more.
I can't think of a single reason not to like Naruto (other than the fact that Sasuke and Sakura annoy me). It's just... wonderful.
Both Naruto and Full Metal Alchemist are some of my favourite anime, though!! They deserve their popularity. :)