Okay my list so far:
Akash has battled: Argent Adept, A/Z, Chrono Ranger, the Scholar, Sky Skraper, and Young Legacy after some form or fashion. He has battled the following in pairs: Argent and Fanatic, Fixer and Ra, Legacy and Expatriot. Teams Battles? Almost certainly the Freedom Five, certainly the Prime Wardens.
Omnitron - It's impossible to know which Omnitron fought who, but individuals that battled a version are Omnitron-X, the Naturalist, Haka and Ra. A/Z and the Bunker have battled him, so that means the Freedom Five. Argent, Parse and Nightmist fought him in tandem, as did Tempest and Fanatic, which puts the Wardens into play.
Iron Legacy - Various Legacies, sure. Parse, Visionary, and Haka took a shot at him. The Sentinels fought him, as did Fanatic and Tempest (meaning probably the Wardens), Fixer with Argent and Expat (probably the Dark Watch... 1 huge battle?). The Freedom Six obviously fought him (and lost) and Wraith (POF) also fought him with Horus Ra (which suggests a change in Ra's future based on Tactics, right?). IL is defeated by Tachyon, Tempest, Fanatic and Nightmist, which is damn close to an ideal team to take him out.
Voss - Argent, Expatriot, Haka, Nightmist, Scholar, Tempest alone. Wraith, Visionary, Haka and Tachyon fought him together, as did the Freedom Five, unless Haka just joined them for that battle.
Dreamer - Was this just one incident? Argent, Legacy, Tachyon, Chrono Ranger, Scholar, and Wraith were involved in some fashion. Nightmist and Sky Scraper worked together for this one. Obviosly Visionary, too.
La Capitan fought the Sentinels, but also the Argent, Nightmist, Sky Scraper, Tachyon and Wraith. Most of those fit somewhat thematically, but Wraith? Hm.
Vengeance villains alone or in a group fought every-freaking-body.
Ambuscade fought Bunker, Chrono Ranger, Haka, Parse, Scholar, Setback, Wraith, Tachyon, Ra and the Argent Adept. Also, he seems to have fought Team Leader Tachyon which implies the Freedom Six. Did he work for IL?
Infiltrator - Captain Cosmic is obvious, but also Tempest, Sky Scraper and Wraith. That's conviniently a great team.
Dawn obviously fought the Freedom Five ond Expat. At other times Chrono Ranger, Captain Cosmic, Knyfe, the Naturalist, Omni-X, Ra, and Visionary battled Dawn. In pairs Tempest and Wraith, Parse and Redeemer Fanatic also battled Dawn. I never thought of Parse with that Fanatic, but I like it. It also means she wore the armor for more than just the Apostate fight. I wonder how long it lasted between original and the PW versions.
Gloomweaver fought the Dark Watch and Nightmist, but also Chrono Ranger and Scholar. Gloomweaver in game doesn't merit that much firepower, but in story...
The Alt Gloomy and Spite - they fought the Dark Watch and the Sentinels.... that's pretty cool, no? Team Team-up!
Plague Rat wanders around being gross fighting Chrono Ranger, Sky Scraper, Fanatic and Bunker. Bunker usually means FF, right? It seems likely since Tachyon definitely teamed with Legacy against the Rat. Visionary, Fixer and A/Z fought the Plague Rat in the most random team up ever. Wraith and Ra beat up on a giant mouse. And I like to include future Haka here, but that's fairly random.
Baron Blade with his Terralunar Impulson Beam fought the FF with Tempest and Ra.
Bomber Blade fought Expatriot, Fanatic, Guise, Nightmist, Scholar, Sky Scraper, Unity, Visionary and Guise... unless there are more Blade schemes we don't know for sure.
Apostate obviously fought both versions of Fanatic, but also the Naturalist, Nightmist, Omnitron-X, and the Scholar. Redeemer worked with Parse, likely to finally defeat Apostate and send him to the Block.
The Chairman and the Operatifve fought the Dark Watch, Rook City Wraith, Fixer, Fanatic, Legacy, the Naturalist, and the Sentinels.
Matriarch fought Haka, the Naturalist, and naturally Tachyon. Parse and Captain Cosmic worked together against her.
Deadline battled Naturalist, Sky Scraper and Parse. That's a team I can't wait to run, though I'll add a fourth.
The Ennead fought Ra at least twice and in between fought the Freedom Five and the Sentinels. They also fought Omnitron-X, Sky Scraper, Unity, the Argent Adept, Legacy and Bunker although obviously the last two vould have just been a Freedom Five battle. Omnitron-X and the Argent Adept would make fantastic partners for Unity and Sky Scraper.
Kismet fought Omni-X, Haka, Ra, Chrono Ranger, Tachyon, A/Z and Tempest. She battled the pairs Setback and Wraith, Argent Adept and Fanatic (Suggesting PW), Fixer and Nightmist (suggesting DW).
Ms. Info - the Freedom Five are obvious, but she also messes with Parse, Unity and then as a duo, Fixer and Tempest.
Spite fought Wraith, Parse and the Sentinels. That seems too few, but I guess a serial killer is below many of these guys pay grade.
Kaagra - Sky Scraper, Tempest, Tachyon, Argent Adept, Scholar, Expatriot, Chrono Ranger, Knyfe and Haka... the title cards.
Progeny fought Sentinels, Chrono Ranger, Argent Adept,and Knyfe. He fought duos of Scholar and Expatriot, Parse and Captain Cosmic, Tachyon and Tempest. Legacy, Nightmist, and Dark Visionary also battled Progeny. I really want to know more about Dark Visionary.
I also have a list of various Hero teams and where they fought, but I think I've typed quite enough. Right now, we pick a villain then draft heroes based on the scnario we want. Hope this helps you guys with new combos and ways to play too.