I wouldn't say that maldives or Bali is better than each other,but they are both great in their own way..Bali is becoming a new place to visit ,so u can go their to explore new places.
Your honeymoon is about how both of you feel togther exploring. Any destination works, as long as you enjoy each other's company, with travel just being a backdrop to you getting to know each other emotionally and physically. Bali may have some diversity other than beaches, with mountains, rafting, city life, discos. Maldives may be a quieter vacation with focus on beach and watersports. My pick would be Bali in a quieter setting to have more variety