I assume that you know that you will pay the Canadian tuition. This is quite a bargain. My kids and I are dual citizens living in the US (my wife is a US citizen) and we found that Canadian universities cost less than our in-state public university. This is even considering a very good merit scholarship that we were offered at our in-state public university. The universities in Canada are also quite consistently very good.
It is hard to imagine how to compare Waterloo with Mount Allison other than size, and the quality of Waterloo’s coop program and computer science and math and engineering programs. Being bigger does correspond to a larger number of strong programs, but also bigger classes.
One daughter attends one of the small universities in Eastern Canada. First semester freshman year she had two classes with 15 or fewer students in the class. You can get to know your professors when the classes are this small. Her biggest class at the time (freshman biology for biology majors) was 90 students. I am not sure if this is the largest class that she ever had in four years. She graduates in May and we are a bit concerned that we might not be able to visit at the time.