The Mi-go are probably the biggest “minor” faction. Right now you are mainly seeing their scouts and explorers while they try to figure out what particular chunks of land they want to take; once they do so they will probably push for those areas hard to secure them before anyone else can react. In my opinion the kreck are one of the big Mi-go subhuman intelligence slave races that have been mostly enslaved (though there are still plenty of wild ones out there).
Grackens have always been a minor faction IMO, though they don’t really have enough clout to claim any of our world themselves. That said they have a pseudo-truce with the Mi-go where they are welcome as traders, etc., in the Mi-go cities (along with a large variety of other semi-unknown races; as long as you have been “recognized” by the Mi-go you are welcome to trade and live in their cities… assuming you don’t do anything to piss off the Mi-go overlords).
Then there’s the Big 3 that we’ve encountered and discussed quite a bit (i.e. the goo/blob, the Mycus, and the Triffids).
There’s also the shadows, who are sort of the new kids on the block (besides us, that is). As best as we know they were from the other “side” of our dimension from the Nether, so this is the first time that anybody, Nether denizens included, has met them. They aren’t having much luck staying on our side yet due to the fact that sunlight kinda melts them (or forces them back to their home dimension, we aren’t sure) but they have had a few times where they’ve infested underground areas. Nobody knows much about them or has really managed to communicate, so they are definitely still an unknown wildcard in the situation (though they are pretty limited to sunlight-free areas, which limits their ability to control ground pretty drastically). I think it might be interesting to potentially have something similar to the Necropolis, but instead of the whole place being filled with irradiated wanderers the whole place (aboveground houses included) is filled with shadows. It’s perfectly safe to wander around in the daytime (including looting near windows), but go someplace too dark or try to do something during the night when all the shadows boil out of the earth would be suicide.
That’s all the real “factions” we have ATM, though there are a few other groups that might be worth noting:
The cultists - These guys are weird. They seem to have some sort of relationship with the blob, but they’ve also definitely been in touch with other factions as well; most likely they can’t accomplish anything here other than be creepy atmosphere guys, but they do exist.
The horrors - This is the amigara horrors, the breathers, and few other of the spooky (usually references to other games/etc.) things. They are usually pretty powerful, but are almost always linked to a specific location (such as the fault lines). These things are native to earth, and have been here for as long as anyone can remember; and they will most likely continue to be here even if something else conquers the planet completely. That said they most likely won’t have any real influence in the long run due to the fact that they are linked to areas, and the fact that said areas are usually just as deadly to humans as they are to other things.
I’m glad you feel that way. I actually drew on the colonization of the Americas as some of the inspiration for stuff that’s there, and the fact that you are feeling that way is definitely a good sign about the lore IMO. 
