You just need to adapt to the buttons, I used to have difficulty boosting and flying the Banshee but now I don't, becuase I fly it often. As for dual weilding, it is very hard to use with Bumper Jumper, I personally don't use it so it does not really effect me much. Just practice with it.
Also, Bumper Jumper was meant to be the "Default" for Halo 3 because of the new controllers and bumper buttons, but because more people are acustomed to Default they kept it in.
I highly doubt they will change the Bumper Jumper scheme.