Here is a MOSTLY comprehensive list of character affiliations. However, due to what I assume is some sort of bug, you can only see the character affiliations when you’re looking at your own roster, they don’t show up when you’re viewing a character on another person’s team or a cover in your queue, so I wasn’t able to get to everyone because there are some characters I am missing. I have all of the three star characters, so that list is complete, but I am missing two five stars (OML, Spider-Man), five four-stars (Professor X, Quake, Devil Dino, Miles, and Drax), one two-stars (Bagman) and pretty much every one star besides Iron Man (and I had a Yelena and Storm in my queue that I added briefly just for the purposes of this list).
So if someone else is feeling helpful and wants to tell me what the affiliations are of the characters I am missing and can help fill in those gaps, I will add them to the list, and once I have them all I will make a second list that is divided by category (e.g. Here is a list of every character on team Team Cap, every character on Team Iron Man, every character listed as a villain, etc).
EDIT: OJSP filled in the gaps for me so now the list is complete!
Master list of character affiliations
Acronym list
IM: Team Iron Man
Cap: Team Cap
DA: Dark Avengers
GOTG: Guardians of the Galaxy
FF: Fantastic Four
Five star characters
Silver Surfer: Heroes, IM
Phoenix: Heroes
OML: Heroes
BS Spider-Man: Heroes, IM
Green Goblin: Villains, DA
Steve Rogers: Heroes, Avengers, Cap
Iron Man: Heroes, Avengers, IM
Four star characters
Ant-Man: Heroes, Avengers, Cap
Carnage: Villains
Cyclops: Heroes
Deadpool: Heroes
Devil Dinosaur: Heroes, Cap
Drax: Heroes, GOTG, Cap
Elektra: Heroes, Cap
Ghost Rider: Heroes, Cap
Howard The Duck: Heroes, Cap
The Hulk: Heroes, IM
Iceman: Heroes
Invisible Woman: Heroes, FF, Cap
Iron Man: Heroes, Avengers, IM
Jean Grey: Heroes
Kingpin: Villains
Miles Morales: Heroes, Avengers, Cap
Mr. Fantastic: Heroes, FF, IM
Nick Fury: Heroes, Avengers, IM
Nova: Heroes, Avengers, Cap
Professor X: Heroes
Quake: Heroes, IM
Red Hulk: Villains, IM
Sam Wilson: Heroes, Avengers, Cap
Spider-Gwen: Heroes, Cap
Star-Lord: Heroes, GOTG, Cap
The Punisher: Heroes, Cap
The Thing: Heroes, FF, Cap
Thor: Heroes, Avengers, Cap
Venom: Villains
Winter Soldier: Heroes, Cap
Wolverine: Heroes
X-23: Heroes
Three star characters
Beast: Heroes, Avengers
Black Panther: Heroes, Avengers, IM
Black Widow: Heroes, Avengers, IM
Blade: Heroes, Cap
Bullseye: Villains
Captain Marvel: Heroes, Avengers, IM
Colossus: Heroes, IM
Cyclops: Heroes
Daken: Villains, DA
Daredevil: Heroes, Cap
Deadpool: Heroes
Doctor Doom: Villains
Doctor Octopus: Villains
Gamora: Heroes, GOTG, Cap
The Hood: Villains
The Hulk: Heroes, Avengers, IM
Human Torch: Heroes, FF, Cap
Iron Fist: Heroes, Cap
Iron Man: None (likely due to glitch)
Kamala Khan: Heroes, Avengers, Cap
Loki: Villains
Luke Cage: Heroes, Avengers, Cap
Magneto: Villains
Mystique: Villains
Psylocke: Heroes
The Punisher: Heroes, Cap
Quicksilver: Heroes, Avengers, Cap
Ragnarok: Villains, DA, IM
Rocket & Groot: Heroes, GOTG, Cap
Sam Wilson: Heroes, Avengers, Cap
Scarlet Witch: Heroes, Avengers, Cap
Sentry: Villains, DA, IM
She-Hulk: Heroes, Avengers, IM
Spider-Man: Heroes, Avengers, IM
Squirrel Girl: Heroes, Avengers, Cap
Steve Rogers: Heroes, Avengers, Cap
Storm: Heroes
Thor: Heroes, Avengers
Vision: Heroes, Avengers, IM
Wolverine: Heroes
Two star characters
Ares: Villains, DA, IM
Black Widow: Heroes, IM
Bullseye: Villains, DA
Captain Marvel: Heroes, Avengers, IM
Daken: Villains, DA
Hawkeye: Heroes, Avengers, Cap
Human Torch: Heroes, FF, Cap
Magneto: Heroes
Moonstone: Villains, DA
Spider-Man (Bagman): Heroes, FF, IM
Steve Rogers: Heroes, Avengers, Cap
Storm: Heroes
Thor: Heroes, Avengers
Wolverine: Heroes, Avengers
One star characters
Black Widow: Heroes, Avengers, IM
Hawkeye: Heroes, Avengers, Cap
Iron Man: Heroes, Avengers, IM
Juggernaut: Villains
Spider-Man: Heroes, IM
Storm: Heroes
Venom: Villains, DA
Yelena Belova: Villains, DA