Will we see military conflicts break out with other Martian colonies and perhaps some mean ass aliens?
From a mod, I really hope having aliens show up is a thing that can not only be done but that the potential to mod this in is a part of the game. As a DLC like the Sunset Invasion in CKII, it would be a good thing too.
I hope that it doesn't end up in the base game though in terms of sentient aliens showing up and playing a role in the game. Alien bacteria or mosses? Absolutely that should be in-game. Just not little green men with antennas that perform psychic readings and fly around in UFOs.
As for conflicts between colonies, Mars is going to be such a harsh and unforgiving environment that anything other than minor sabotage or espionage is going to be realistic in terms of any sort of early game settlement. Competition for resources? Absolutely. Espionage to uncover resource maps of a neighboring colony.? almost invaluable and inevitable. Large scale warfare between colonies? I'd say not a chance in terms of any sort of realism to what the political situation would be like.
Think here more like what it was like in the Americas in the 1600's. Yes, there was some competition between the various major world powers, but battles between colonies tended to be minimal. Even think about what happens in most EU IV games, where more often the competition for colonization is to see who can get the colony going first and spreading colonial influence for your nation before somebody else can get a toehold on the area, with conquest of the colonies is very much a late game thing if it happens at all. That is exactly the kind of situation you will be seeing on Mars.
As a very late game development when colonies are really large but perhaps running out of a specific resources and a neighboring colony not willing to trade.... that might create room for combat. Simulating what happens if war breaks out between the "mother countries" that sponsored the various colonies might also be interesting.... but again that would be mostly colonies trying to stay out of harm's way and letting issues on the Earth remain there.