(At the time I recommended my son start doing Math Academy, I had done 3722 XP myself, which is about 60 hours' worth.)
It's true that there's a stronger emphasis on procedural fluency than on conceptual understanding. But honestly I think that's good: there's so much good material online for conceptual understanding.
Imagine you're studying linear algebra: use Math Academy for rigorous introductions to topics and exercises and feedback, and watch 3Blue1Brown videos for conceptual understanding.
For younger kids (my son is 8.5yo) I wish Math Academy had some animated or video explanations. For example, the prealgebra course includes the product rule for surds. It was hard for my son to grok based on reading the written explanation. Not because the explanation was bad, but because my son has the attention span of an 8.5yo. So I spent a few minutes walking through that same explanation with him, using a paper and pencil to guide his attention.
I also wish they had a mascot and a streak feature. Those features on Duolingo somehow help to motivate my son.