While I would love to play the Braska story (although you know it's coming with a sad ending).
I think that the issue wasn't who they followed as the main character, but rather their lack of attempt to make a storyline.
The entire game was basically side quests, with a peppering of plot. I think Yuna's story could have been a lot more interesting than they made it. I'll never forget my reaction at the end, when Tidus tells Yuna she looks different, and she responds something along the lines of, "Well a lot has happened while you were gone". I was just sitting there thinking "... Not really..."
I will say that I didn't dislike the game. At first I found it really annoying, because I kept waiting for the story to start. Then it dawned on me that wasn't going to happen. After that I was able to enjoy playing the side-quests for what they were.
The point being: I'm pretty sure I would have felt the same way about it if it had been Braska running around doing nothing but side quests until he sacraficed himself. While the potential is there for an amazing story, following Braska - the potential was there to create a great story for Yuna, they just didn't do it.