My vote is for most of the Navis Primer. Heaping more goodies such as familars and soul ward on top of the already powerful Astropath. Fleshing out the Navigator Houses doesn't make the rest of the book worthwhile.
Also, stacking macrobattery salvos. They make lances all but redundant. I'm seriously considering adopting some or all of the Mathhammer fixes to make ship combat not about insta-kills.
What do you find too easy to break in Rogue Trader?