I have a height problem with my girls, they are almost 4 years apart. Usually when i have them stand side by side, I ask the older one to bend her knees {just a little} and I've found that shooting from an angle can help as well.
This is one with two examples... the older looking down on the younger is a cute pose and then having the older kneel for one shot at least gave a different pose than always having her towering above her sister.
You can also use a prop for the younger one to sit on that would get their heads at a somewhat equal level, like this