The first anime had a very dark story , with the action led by the main characters. It follows the manga up to the half of the story and from there is just filler. What I liked at the first series was the dark tone of the story and the sad ending. I didn't like the fact that Winry personality wasn't truly developed through the series, the fact that we have a small cast of characters and the plot twist at the end. The idea behind the plot twist wasn't bad but it didn't go well with story and it didn't explain exactly the meaning of the gate and of the alchemy.
The second anime that is an exact adaptation of the manga from the beginning to the end has a much complex story with the action led by the plot. In this remake we have a large cast of characters that are developed better than in the previous series, in the remake Winry is much more down to earth so to speak than in the previous series. In FMA Winry is just about automail but in the FMAB we see that she has feelings for both Elric and Al, especially Elric. I like the end of the remake because it show us the meaning behind the gate and because it is a happy one, and to be honest they deserve a happy ending :D.
I like both anime series but because the second one has a much better plot with characters better developed (being based on the manga) the second one goes in my Top 5 and the first one doesn't.
