Things that could be modified by racial ability:
Research/Wealth/Trade point generation
Mining rate
Mining accessibility
Survey points
Cybernetic/Diplomacy/etc skill
Tracking speed
Engine speed, efficiency and signature
Weapon ranges
Power generation
Ground combat strength
Training
Unrest level
Population protection requirement
Cargo loading speed
Cargo capacity
Fuel capacity
Terraforming rate
Political rates (i.e. quicker/slower to Imperial status)
Maintenance failure rate
Maintenance clock speed
Ship order response time
Population "breeding" rate
As I was typing this, something just occurred to me though. There're so many things that can be tweaked, it might be over complicated (both to setup, balance and program), so how about something like the Civ 4 leader traits, so a Militaristic race might get better crew training rates, officer generation, tracking speed, etc., Expansionistic gets quicker pop expansion, faster ships, etc.
You then have a matching negative package, e.g. Pacifistic
Race setup is then baseline, with an option to take one advantage and then one disadvantage package. Or maybe baseline, with one free advantage package and the option for more advantages but you also have to take a disadvantage for each extra one.
Stephen