POSSIBLE SPOILERS WARNING
the 2003 anime is my favorite, yes the manga/brotherhood storyline is still good but i liked the first anime the best. i thought that, for making an anime based on a manga that wasn't even finished yet at the time of it's creation, that they did a pretty good job with the direction they took it, people couldn't have expected a lot of the things that showed up in it. i liked the homunculi better in that version, how they were made, their backstories, everything. yeah a lot of them were the same but still, i loved seeing how they interacted with their pasts and creations effecting them throughout the storyline while still being very human in their own ways. to be honest, i even found Dante, despite how much i absolutely hate her, to be a wose character than Father. honestly, his entire plan is a little redundant and expected, isn't it? killing hundreds and thousands of people over the years just to live forever and stay young and beatiful? far worse in my opinion.
there were fewer characters and some missing, yes, but those who had minor roles to start with like Rose were given bigger ones later ona nd you got to see them have their own strengeths as well just like the other characters. everyone still had a challenge and difficulty they had to overcome and managed to develop throughout the storyline. true less time was covered in that version it seems but it everyone still had something to get past. the art and music was still good, and i had far more emotional responses to the 2003 anime than brotherhood and the manga. yes the manga and brotherhood had some moments where i cried but i cried, felt scared, was on edge, and felt what the characters were expressing more in the 2003 anime. yes the ending was a bit saddening, since Ed and Al were separated but it worked for that storyline and what they did with it. Shamballa really wasn't all that bad either. again, not a perfect ending and what everyone was hoping for but it worked for the storyline it was given and sometimes animes don't end or turn out how we want them too
over all, both of the versions were good, but the 2003 anime is still my favorite for those reasons and a handful of others. these here are just the main, big points