At the time, his career was on the skids and he was persona-non-grata in the movie industry. Had he had the balls to ask for more money he would probably not have gotten the part.
Addtionally, nobody knew it was going to be 'such a hit'...not Paramount, not FFC.
I think that in the financial sense, everything worked out fine for Brando the way it did.
The reason he didnt come back for the flashback in 2 was becuase he believed he had gotten screwed by Paramount because the movie did become such a big hit and he felt he got the short end of the stick.