I think 03's smaller scale allowed for greater focus on the brothers themselves, and there's just way more development for the homunculi, since in Brotherhood they are mostly viewed just as henchmen (granted Wrath is more interesting). I think also plot points are allowed to sink in a lot better because of how the show's paced. In Brotherhood, it seems like the show can never keep a serious moment serious without interjecting some form of comedy (later in the show it becomes a bit better at this, but it still is sometimes a problem). 03's changing of certain plot points are also a lot more interesting.

People are also very quick to write off the show because of "Robo Archer", which honestly, that character is a tad silly, but it actually does fit within the context of the show's world. The whole point of Robo Archer is to showcase the experimentation of new automail technology, in this case, one that re purposes a human being more so into a weapon. That he'd do anything to rise in the ranks, even sacrifice his own humanity. The fact that he goes insane from this is kind of the point. The dude lost like half his brain, and didn't even go through automail rehabilitation, lol.

Even in terms of "filler", only one episode in the entire show's run actually does not advance the plot in any way, and that would be episodes 4 & 10. The rest of the series, even the comedic episodes, have moments that add to the story and to the characters.

So yea, that's pretty much why I like it as much Brotherhood. That's not to discredit what Brotherhood does, since I think it crafts its own interesting narrative as well. I also highly recommend goat jesus for a more indepth breakdown.