1) outposts are smaller than colonies. Yet, a colony ship requires a pop between 1 and 999 and an outpost ship requires pop between 3 and 999. Thus, I can build colony ships on a planet with a pop of 2, but not outpost ships.
Fixed revision 4881 "equalized population requirements of colony and outposts."
3) a way to tell that these natives cannot build colony ships (I ran into the problem with Abaddon...somethings)
Check the pedia to see what minor species can do. Abaddonni can build colony ships, so you must be missing another requirement, such as shipyards.
4) maybe an ability to eradicate the pop of the captured planet and put own species in their place?
The concentration camp is supposed to do that i think.
EDIT: 5) unused resources - above a cap set by the player - transformed into Trade/Influence
Since trade/influence doesn't have any role in the game yet, to add that now would hurt the player.