The faction imbalance could have been made trivial from the start of development. It should be a relative issue rather than an absolute one.
In war, ALL soldiers are fighting against the enemy.
2 sides, A & B.
doesn't really matter if side A are imperial and side B are also imperial, relative to side A's perspective, side B are the republic and vice versa for side B, A are republic.
This requires symmetry and symmetry is a good thing, it means balance.