I could care less about the manga with the first one, I knew it wasn't going to follow the manga but there's something the first one had that the second definitely lacked and perhaps it's because it stuck to the manga. If the second anime had a proper score, decent vocals and better dialogue (something the first had in abundance), it would've been closer to call.
However, honestly, I feel as if FMA (The 1st Anime) was so gloomy and lurid that it was an absolute perfect depiction in respect to how reality is and that's why I loved it. When a hole gets blown into your life, things don't return to normal, there aren't happy endings and people talk about closure, but really the truth is, life doesn't change if you don't work at it. That was the basis of one of the many strong themes they had going for the story in this anime.
There are so many messages and underlying themes to that anime, outside of the historical accuracies and references the ended up meshing into it, they made that anime more tangible than any anime I've ever seen before (aside from perhaps Death Note to some extent). Not only is that anime, (FMA1), one of my favourites but it's been vying for the top spot for the longest time and if not for Cowboy Bebop, it would be there.
The characters seemed much more authentic, vivid and had multi-dimensional feel to it. Character development throughout the series felt more akin to life than a tv show. Point I am trying to make is that it was able to convey a really well-rounded story, something that most anime struggle with. Not to mention how they accurately described the people of Ishval/Lior and gave them a culture intertwined based upon our historical events gone awry.
The story-line for the anime was simpler, more realistic and for all intensive purposes better. It conveyed the one true point about greed and malice, both of which hinge on humans and that no one but humans are responsible for the actions. Sure the homunculi were present, but they were all created by Dante and thus roping in the whole truth about the world we all live in.
You can compare them all you like, hell they can make six or seven spin-offs or completions to that manga but the way the original anime adaptation/adjustment took place, those writers clearly had their audience in mind. Could the ending have been happier? Yes. But I like the way they ended it. Even though it wasn't your happy-go-lucky ending everyone wanted, Edward/Winry weren't together but they stuck true to the story.
Now when you include how incredible the score was for that and how well the English Voice Actors performed, you have yourself a masterpiece among masterpieces. Just because it didn't follow the manga, didn't make it worse, I think for that very reason it made it better. The writers/animators were free to do what they wanted and how they wanted the story continue, it just so happens that they were able to contrive something really good.
All you can really say about the second anime (Brotherhood) is that, well it was more shonen-like and it followed the manga, so you can see it competing with Naruto, DBZ, One Piece, Bleach and all the other shonens. But also, I'm not a fan of the humor that was used in it either. Not to mention a shoddy score, I expected something better perhaps more of a orchestra-like performance and well the story was really rushed (more-so) than the first FMA.
Full Metal Alchemist (1st Anime) all the way.
