You mean other than size and price?
I bought my used CX-3 because it is smaller than the CX-5 and gets better fuel mileage. I was also able to get the AWD GT model for less money than a comparably equipped CX-5. I'm sure there are many other differences on options and features, but I was looking to get the smaller sized vehicle after driving a Tribute for 10 years.
Now that the CX-30 is out, I might have an issue at replacement time because it seems to be a blend between the CX-3 and CX-5.