I've been told my BMW mechanics to think of the N55 as a cost reduced version of the N54. BMW simplified the design, cut out some of the high end components (i.e. piezo fuel injectors, dual independent turbos) and traded off raw performance for ability to better control fuel consumption.
N55 still uses HPFP, but design has been improved. N54's with latest HPFP should no longer experience high failure rates. My E90 MSport is still on its original fuel pump. The 2010 DME reprogram is said to address this issue.