Heros vs Villians can be a frustrating game mode if your team doesn't work together. The strategy to win is to stay together with your team so no one gets ganged up on. If possible play a lightsaber character as they dish out the most punishment. I also recommend this mode for grinding out We are the Spark (500 destroys with heroes). You will certainly get this if going for the completion.
To actually get the win your team must kill a "marked target" Ten times before the other team kills Ten targets on your team. Both teams get a random player marked and serves as a beacon for the other team to attack. After a target is killed there is a ten-second countdown for both teams and a new target is selected.