Hiya,
First of all, Milotic does not heal ex's. That's why it doesn't really help if your opponent that uses lotsa ex. Secondly, Meganium can do Toxic. After healing, you still have a fresh Queen, with a Poisoned defending Pokemon. Thirdly, Queen's second attack can pretty much ko any Pokemon, even ex's. With Full bench, it can do 100 each turn.
And...Milotic is not use as often as you think. Milotic is used only when you are in tight spots, or when you really need it.
cya/