Possibly a dreadful idea, but I've seen a lot of complaints about the ST aptitudes.
-Take away one of the aptitudes it has already (I would suggest fieldcraft, but you may have your own opinion).
-Allow players to choose (or roll randomly for) another aptitude at character creation (with the obvious exception of Psyker).
This way, each Storm Trooper can become a specialist within a specialisation. Take the weapon skill attribute for a CQB specialist, or Tech for demolitions/Splinter Cell-type-guy.
Just a thought.