I remember when Brotherhood was at the top of the board back in 2009. The watch threads were pretty comfy with lots of effort posting. In hindsight i would have to agree with the old toonami f/a/gs that it wasn't really better than the 2003 version. The biggest copout argument back then was "It follows the manga" and the action. And it was a pretty well animated show, no arguing that. The board traffic was reaching levels only seen back when the first Eva rebuild dropped.But on its merits compared to the 2003 version, it falls short.
To me 2003, had better character progression, better plot strucutre, better tone, better overall theme. It's a smaller cast and the main focus is on the Erlic brothers and theri journey, making them more rounded characters. Even the filler made brought alot of character to the Elrics.
The the idea of the homunculus creation was better - failed transmutations ment to bring the dead back to life is much more impactful as a plot point, than the Father discarding his sins. The homunculus weren't just hired goons, they were failed beings tortured by their existance. Thematically they all represent their sins, they represent the hubris of their creators. They are tragic figures and not just some bosses for the MC to farm XP.
Unlike in FMAB, the core idea of equivelent exchange is constantly challenged throughout the show, right down to the antagonist calling Ed out for his core believe - sometimes life just happens and you don't get what you want, no matter how much effort you put into it.
Dante is a much better villain then Father simply by the fact she is petty and selfish - her desire to live forever makes her human. Father wanting to be God because reasons, on the other hand, makes him come of as generic villain, for villany's sake antagonist.
The side characters are much better fleshed out - we don't simply jump from one action scene to the next, leaving no room for actually having to care about them. They are not there simply to full out the epsiode. Martel is not a one note character - her interaction with Al and her eventual death are part of his development. Nina's death is not a one note event ment to move the plot
Another point in FMA2003's favour for me is the action - it's serves the story and theme of the show. Ed's fight with Envyh is short and to the point - Ed doesn't just magic a big rock from the ground to smash his oponent, no he uses his knowledge. The same in his fight with Sloth, which to me is the series' peak, especially with Bratya playing as the background.
The tone of 2003 is much more consistent, while FMAB and it's chibi humour completely ruins scenes that are ment to be important. Ed doesn't make silly faces during his battle with Sloth. Mustang isn't making jokes while battling Pride. Barry the rippper is not played as a joke.
The ending i find arguably better - Ed doesn't punch God with the power of frienship and he doesn't get the happy ending. In the end he commits to his beliefs - even if it might not work out, even if he might not get what he wants, Ed will still give it his all. He still believes that if you give something of yourself, you'll get something in return.
Bottom line. I have not rewatched any of the adaptations in 10 years maybe, but the 2003 version still sticks with me way more than FMAB.