I believe this has been proposed at least once and received mostly negative feedback.
A second wave in Daily Challenges, GBG, GE and Event quests is there to make the fight more challenging. Players who can't beat a two wave army can either work on boosting their attack stats, negotiate (in GE and GBG) or do an alternative quest which is always offered in Event quests.
As far as PVP goes, if both the attacker and defender had a two wave army, it wouldn't be easier - it would just take longer to finish the fight, that's why I'm against it.