Just going to throw my two cents in: There were a couple ideas that I appreciated in the thread yesterday, that I think should be used:
-The natives once had a highly advanced civilization, that has since fallen. (Perhaps the majority achieved transcendence, maybe there was a great war, who knows.) Because of this, Alien ruins become a usable resource. You can investigate ruins, and potentially gain tech, or unleash some ancient defense system.
-Native units (tribes, kingdoms, whatever) provide a separate bonus for making nice with them, including potential military units comprised of natives. (The thought I last saw was each tribe essentially opening a tech tree.) Which would require a few ideas of what sort of "factions" exist within the native populace.
Personally, my current idea is that, long ago, Tau Ceti's population got to "lolwhatever" levels of biological and genetic (re)construction. They built their perfect society, and sailed off into the stars.
When the human vessel got to a point about (however many we want) years out from the planet, it activated some sensors. Those sensors activated defensive cloning chambers. Some of the chambers created huge warriors, others diplomats, and other nimble saboteurs. The chambers were meant to bolster the world if invasion was imminent.
The problem was: the chambers didn't include very much in ways of education, as there were supposed to be people standing ready to teach these people. As such, only some basics were maintained, such as ingrained weapons memory for the warriors, and an instinctive dislike for attention among the saboteurs
So when the humans arrive, they find the planet bustling with aliens, who don't recognize each other, and don't recognize the new guys.