Exodus is a pretty simple mission, since the only ship you actually need to protect is the Harvester. The challenge comes from protecting as many civilians as possible.
Three tips should get you through:
- each Shadow attack waves goes after different civie ships. If they destroy their target, they aim for the Harvester. So, prevent that.
- try intercepting a wave (for example number 1 or 2) before they even reach their target.
- call for reinforcements early.
By the way, this mission is going to be a little easier in the new release bundled with 2261.