On one hand, I agree with you - the plot doesn't really take off until that quest takes front and center. However, what's so crucial about that beginning section is it hammers home the main characters' personalities and establishes emotional stakes. Those beginning episodes are the fuel that sustain the rest of the show. And yeah, there's a few filler episodes in the beginning, but they still address the show's thematic elements and develop Ed and Al as characters.
...but when comparing the episodes after Laboratory Five, Brotherhood wins by a mile. No question.