In my opinion home world aptitudes do not work. See here for reasonings http://community.fantasyflightgames.com/index.php?/topic/114226-psi-power-re-reqs/
What I will be doing is removing the stat aptitude you get from your Home World and give each PC a stat aptitude pick of their choice. So if you want to be a perceptive feral or a tough noble you can.
Thank you cps and Fgdsfg for helping me to arrive at this conclusion
I don't think it's necessary to completely homogenize the homeworld aptitudes. Giving players a little more flexibility would help them make the characters they want to make without feeling penalized by their homeworld choice. To that end, I let my players select a home world aptitude matching one of their "plus" stats. For example, a Hive Worlder could have either the Agility or Perception aptitude.
Also, don't Astra Telepathica psykers essentially get a free Characteristic aptitude of their choice? They get Psyker from both their background and their Psyker elite advance, so they have a free aptitude to assign to the ability powering their discipline of choice.
You can also check this thread for different ideas on how deal with the aptitude system: