I find it a bit frustrating that cannot swith allegiance from Carnius to Falco in the later stages of the EEC questline, if you chose to side with Carnius at first.

During my first playthrough, I found it wasn't obvious at all that Falco was the good guy; after all, he has no proof of what he advanced. So being loyal to Carnius seemed the logical and sensible thing to do.

OTOH, it does become obvious once Carnius orders you to assassinate Falco; at this point I really regret the devs didn't give the player the opportunity to betray Carnius and side with Falco.

There was probably a hint of who was really concerned about the colony when you first talked to Falco and Carnius. One asks you to help keep the other's corruption in check. The other one offers you power and wealth. One gives you quests that are more of the light-side good and fuzzy kind. The other one gives you quests that are more on the ruthless/cunning/dark side that give you more gold. Of the two, one does seem more concerned with making sure the colony succeeds.

Falco has asked me to help him keep Carnius in check as the colony grows. I should be careful in taking sides, but he wants me to consider aiding him.

Carnius has offered me power and wealth if I help him achieve his goals for the colony. I should be careful in taking sides.