Though I'm no expert the way i see it there are;
-a few special boffs
-traits you want to go for
-abilities you want to go for.
These are normally bind on equip 1 per toon,
includes (but not limited to)
Some of these are rewards from when a storyline was new, or a re-run, the android is (i think 400 day vet reward)
The only way to aquire an unique boff is to have played when the story came out, or if there is ever another Re-run.
There is also a Borg Science officer you can claim after doing a secret accolade (hint: its in a Borg stf AFTER you have at least been to the CESTUS sector)
These are specific boffs available only from the C-store (Z-store) such as a fersan boff for KDF and Aenar Boff for Fed. (not sure on limitations if your allowed more than one) If i rember these are tradable though.
Each boff has 4 traits. Depending on the race of the Boff some have required traits e.g. an orion female always had seductive.
Traits aren't exactly the most important things in the game, but they can give additional help to your Boff away teams. E.G. if your making a SCI boff with strong healing ability, then look for one with the trait "creative" as it boosts healing abilites (along with damage)
Traits are generally random, so picking specific Boffs for traits can take some time.
Certain Boffs come with an ability that is a better rank than anything the skill trainer can give your boff. e.g. Certain SCI Doffs come with the commander ability 'Vascular Regenerator III' the skills traininer can only train up to VRII,
Certain "special" abilities can be trained by other player captains too.
Hope this clears up any questions (and makes sense ^^)