I'd like to see species-specific skills in compliment with species-specific traits.
So, for example, a Klingon BO might have the Bat'leth skill. This skill would allow your Klingon BO to use a Bat'leth in melee just like the NPC Klingons do, without sacrificing a ranged attack. Higher skill levels would increase accuracy, damage and chance for criticals.
Nerve Pinch could be moved from being a Vulcan trait to being a Vulcan skill, allowing Vulcan BO's to employ it in melee. Instead of taking up a racial trait, it would be an optional skill that could be trained up. For Players it would probably remain a racial trait (unless it became a player skill, see below).
Ferengi BO's might get Energy Whip skill. Etc.
We can probably come up with all kinds of ideas along these lines.
So how would a BO acquire these skills?
Well, you could have species-specific skill vendors, of course. That's one way.
Another way to do it would be to give Player Captains the inherent ability to train any racial skills for their species.
Or, give Player Captains comparable racial skills that they could choose to allocate points in. For example, maybe a Klingon PC could allocate skill points in an optional Bat'leth skill that increased their accuracy, damage, and chance to crit with a Bat'leth. With 3 ranks in Bat'leth they could train BO's in Bat'leth I; with 6 ranks they could train Bat'leth II; with a full 9 ranks they could train Bat'leth III.