Did you know that the special Commander abilities can be countered? You know of the Allied Time bomb? you can shrink it to reduce the damage, have Yuriko attack it so it floats in the air and only damage air units, and if you have a Chronosphere you can return the bomb to sender. There is a wikia page showing all of the possible counters to most of the protocols.
Other protocols stack and compliment each other. Empire’s Final Squadron get a bigger punch with Honorable Discharge (units that die explode) and Cryoshot then Time-bomb (nuf said).
More interesting combos below.