It works okay, but you have to be careful with the builds you use to make sure you don't run anything that requires a specific counter.
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Anything that specifically counters both of them or that specifically counters one of them without being specifically countered by the other.
It works, and there are failsafes built into the system (live another day, knowledge is power, the strong adapt, etc.) to make it easier. It's certainly easier than trying to balance other games around 2 people.
Er yeah my bad, that's what I meant by ally. That said I plan on talking with them to see if they'd rather have the allies in question be a permanent ally (inwhich case the allies I'd probably consider letting them build entirely as both mechs and secondary cast members), or if they'd rather allies be the byproduct of various circumstances. (Each of the Major factions will have their own mechs already stated out. While a town militia definitely files under reinforcements. As does admittedly any unplanned scenario since making reinforcements takes all of 30 seconds opposed the 5 to 10 minutes a mech might take.)