As otherwise noted in this thread, it could be a number of factors including the drive-by-wire, wear, master cylinder, etc. I'll also throw in a comment that it can be difficult to drive BMWs smoothly just due to the way that they are engineered, gear ratios, etc.

As for the squeak, I remember that being a common issue with E36 and maybe E46 cars as well. Just spray some lubricant down in there somewhere where the pedal pivots and see if that helps at all.

FWIW, I'd like to thank the OP for the thread. I actually, embarrassingly did not realize that the E53 was ever available with a manual transmission!