What if MOCX were militias sometimes ennemies and allies of XCOM? The world is multipolar. Make your decisions accounting for additional AIs.

On the tactical side, make it more like real life: we could say resistant and opposing groups had their own informant network and were told of coming XCOM mission and decided to help their ally side with their own resources. Let's say, for example, you go on a heavily cramped mission you know is going to be a nightmare. Your campaign is not going so well. And, oh, what is this unknown human group fighting Advent here?

To add some depth let's say, kills by this group don't give you anything, neither XP nor loots, and their IA will act independently yet anticipating their moves so that you will adapt your own strategy according to what you expect will be their move. Of course they may turn hostile when attacked by you (careful of grenades and such)

On the strategical side: add some of these groups with initial havens XCOM could "ally" counting for continent bonus but with a tad different haven management or longer contact time (to balance the thing that is). They could even loose their haven to Advent and ask for exile in XCOM.