The competition's already fair. That's the point. You just got through pointing out that Light's been dominating the mass battles at ToH but that Dark is faring better at these Light vs. Dark WoE castle events. There's your answer, right there: different scenarios = different advantages/disadvantages = different outcomes. There's nothing unfair about it.
People CHOOSE a faction, people CHOOSE to show up or not show up for events, people CHOOSE which character to play as when they participate in events... it's not something you or I or the GMs or any one particular person has any kind of control over. It is what it is. We have to work with what we have.