Dual Builds was a feature in City of Heroes/Villains that I always thought was really great. (Actualy it became 3 builds later on, but let's keep it simple for the time being).
Basically (in STO terms), it allowed you to have two full and separate skill builds.
You could then name your builds to keep track of them
When you wanted to respec, a respec would only work on one of the builds. You would have to swap builds to respec the other build using a separate respec.
Why would this be useful for STO?
1) Players would be able to have a team build and a solo build.
This might lead more players to take something like threat control for when they fly their Cruiser and then if they decided to swap to their Escort they could swap to their Escort DPS build with no threat control.
This in particular has always been a great boon for players that like to play support but end up having to solo a lot and thus don't specialize themselves for their support role.
2) Building off of #1, in the current game environment many players have more ships then they possibly have characters - two builds would allow them to customize for different ship types.
3) More players might spec for a specialized PvP (healer, DPS, etc.) build while keeping a more generalist build for PvE. Hopefully this might lead to less trepidation to hop into PvP.
4) Potential to lead to more respec sales. Now players have two different builds they may want to respec as needed.