In alien-vs.-human combat, use nerve gas. Because there are no interspecies atrocities, the discovery of High Energy Chemistry (which enables Nerve Gas Pods) is as important as learning to build Needle Jets with Doctrine: Air Power.
While playing as the Pirates, nutrients and energy are easy to obtain. Make mineral production a priority at your base locations. Raise your energy production with Tidal Harnesses, and your income will easily rival that of the wealthy Morganites.
The Cybernetic Consciousness steal technologies when they conquer a base and do not have any real drawbacks when playing a military game. They should be played as aggressively as the Spartans or Believers against their weaker neighbors.