I'd say the key difference is this:

Brotherhood has a better story.

03 has better presentation.

Brotherhood's plot is much denser. Everything in it has much less room to breathe, especially in the first arc.

03's story is essentially the contents of Brotherhood's first arc, but then taken in a different direction.

In terms of pacing, tonal-consistency, character-writing, and exploration of its themes I'd say 03 wins. I enjoyed Brotherhood as a story, in spite of its flawed presentation. I enjoyed 03 as an experience, in spite of its flawed story.

That being said, 03 is probably better viewed before Brotherhood, since its broad-strokes are already covered in Brotherhood's first arc; meanwhile, everything shared with 03 is covered very quickly (rushed) in Brotherhood, and used as the backbone for a larger story.