Brotherhood skipped a lot of stuff that was in FMA03 on the assumption that anyone watching Brotherhood at release would have also seen 03 and would know the divergence point, which does weaken Brotherhood to an extent as time passes and more people watch it without 03.
While I feel Brotherhood had a better ending, I still really like the ending of 03. The writers had to basically guess an ending based on an incomplete manga? And they went for a really personal, small stakes ending that lined up with the clues given and I think they did a really good job. Mangahood ended with a giant nationwide crisis and the intensity of the stakes at that point made it clear the home team would succeed. FMA03’s final conflict was so personal that you could believe the bad ending was a possibility, and in some minor ways I appreciate it