The Joined Trill trait will slightly increase your damage from energy weapons and torpedoes, slightly increase your power levels, and will slightly increase the power of Engineering and Science Boff powers.
The Efficiency Trait increases power to your subsystems, but only if those systems are set at less than 70 base power. Assuming you're running a balanced power setup, it will slightly increase weapon power, increasing the damage of your energy weapons, slightly increase shield power, increasing your shield regen rate, slightly increase engine power, making you move a little faster, and slightly increase Auxiliary power, making you turn a little faster and making some, but not all, Science Boff powers more effective. On the other hand, if you're running a 70/70/30/30 setup, Efficiency won't do anything for your energy weapons or shields, but will have a more noticeable effect on your engines and auxiliary power. This is assuming Efficiency is working as intended. As others have mentioned, it might not even function until you have at least one skill level in each of the Commander Efficiency skills.
Considering Warp Theorist doesn't work without at least one skill level in Warp Core Training, I consider it likely Efficient is in the same boat.
Anyways, I would consider Joined Trill to be superior for a Science Officer, as every little bit helps in improving those science abilities, while an Alien gen with Efficient would be better for an Engineering Officer/Cruiser Captain.