I always kind of felt that the ending of Macross Zero was result of sreally still likeof Kawamori writing himself into a corner. The message was kind of anti-war, so I guess a massive battle was a bit contradictory. And it also had to fit into the time line before the original Macross, so I suppose it would have to be a bit vague. 
Some of the events are explained a bit more in Macross Frontier. I do really like Zero though.