I really agree with this, it doesn't belong.
The whole entire girl programmer thing really bugged me. They introduce these two characters, and they don't do much, except eat a plate of donuts. They just solve the code, and that's it. Wow. Yippie ki-yay motherf*&%$#. Big deal. They almost seemed like dead weight to the movie.
I also really agree with this, anything with little miss "I need eyeshadow and a sexy hairdo to work for the government" that can go should go. Especially her little line about "think quantum mechanics", the way she says it you just want to tell her "bitch, you don't even know what that means!"
About the score, some of it I thought was pretty good, but I could do with almost no electric guitar, but thats only what I think. If it's the sort of thing that was part of previous Transformers incarnations I'd keep it (for nostalgia's sake?), but if not I'd let it go.
Also the bit with the soldiers being non-accepting douche bags when they make an issue about the Spanish soldier speaking his native language, the scene very early in the film. I feel it could go.
One last thing (and without it I think the movie would be just great). The bit with the cell phone charge and finding the credit card in the desert fight. I know it got a few laughs in the theater (even a giggle out of me), but it was so not fitting for the scene, it slowed down the pacing so much in a place that could have been near perfect action-wise.
Anyway, I hope some of my thoughts are helpful. I'm definitely interested in seeing how this turns out. Until the next post, I hope your move goes well.