Traits (even the new, buffed ones) aren't as contributing to your character's performance as skills. Skills have those mins and max levels required for space and ground so future content can be made with some notion of the power range all characters will be at. Traits don't affect that power range all that much.
I agree, ditch the classes and allow for primary and secondary career skills, much like you pick the traits at the beginning of the game. For example your primary career skill is tactical and your secondary is engineering. weapon efficiency (DPS) would be increased when using a "cruiser" or "science" vessel, and because of the engineering secondary it would supply a turn rate boost to cruisers. There's WAY too much different in stats between the different ship types and among the various ship class abilities/setups. Bringing the ship class stats closer together and having all universal bridge officer stations would allow for so many more options.
There's no good reason why a good ship captain can't go down to engineering and help realign the plasma injectors and then go down to the science lab and help with an analysis of a biomimetic compound, but still be able to formulate some solid battle strategies when needed, or any variation of that.