I forget the names so I'll just describe it the best I can.
1. Three control points. One near each team's deployment, and a third in the center that could only be held by a warlock/warcaster.
2. Kill Box. And in addition there's like an 8x36" area that you have to contest/control.
3. Capture the flag type scenario with reinforcements.
I think when it comes to theme I would make this sole edit: If you play the same faction then you are considered to be friendly faction models. If you don't then you are considered unfriendly.
The only team made up of two lists of the same faction was the team that only had one player. Obviously there's a lot of synergy within a faction, and having two casters of the same faction is advantageous. But I don't think its any more powerful than adding a caster and units to round out your army/faction and do what it doesn't do naturally.
I mean Danny and I combined pDenny and pHaley. What doesn't Cryx do? It doesn't soften things up well from afar and lacks ranged utility. No problem, Cygnar will pick off anything annoying and cover the advance so life's easier for you in melee. What's Cygnar missing? The ability to consistently make the innumerable POW 10's we spew count. Well, thanks to spells like Parasite and Crippling Grasp that problem is solved.
And like I said before, what about mixing a caster with lots of KD effects (pKreoss) with a ranged assassin (eCaine)? What about someone who can trap you in place (eDenny) with someone who will murder you in melee (eStryker)? What about doubling up on casters that don't allow you to do anything (Harby & Old Witch)?
Armies are capable of being obnoxiously gross even with the caveat of not being friendly towards each other.
You could go either way, Sean. I guess that all just comes from a theme perspective, and also not really seeing what uncontrollably broken in-faction combination it kept from hitting the table.