The first series started inn 2003, and studio who created it asked Hiromu Arakawa (the woman who created, wrote, and drew the manga) if they could voluntarily alter the storyline so it would end differently. Therefore, there are slight differences which are introduced early on, but which grew stronger as that series progressed. Ms Arakawa actually told Bones Studio everything, because she knew the story arcs she had planned, and how she planned to end her story. The 2003 anime came out, and had an English dub as well, which brought more people to the manga as well.
Cycle on to about 2007, when talks between Bones Studio and Ms Arakawa resumed. Bones wanted to do Brotherhood, as it came to be known, because the story was different enough. However, as the first part of the story is largely the same, Brotherhood skims through some of the early stuff (at least one story, comprising an episode in the 2003 version, is "covered" at first by one line of dialogue from Lt Havoc, although the main character of that story tells "his version" of the story later, although picturing Ed primarily as a villain). Bones persuaded Ms Arakawa to let them do Brotherhood, even though she was still writing the story as they were animating and recording Brotherhood. In fact, if you watch carefully, you can see minor differences between the final two episodes of Brotherhood with the last chapter of the manga, because Ms Arakawa's final chapter was published very close to the time of airing, so she could only tell them what she planned, not show them page by page what she had done.
Sorry to be a pedant about it. I really love Brotherhood, but I do think the 2003 version is truly wonderful, and a lot better than many other anime out there. Hope this helps?
500
200
100
